I've updated my fishing farm for 1.4! It's bigger than the pre-1.4 version, but the results are awesome:
The idea is that you stand on a platform to select your biome, then fish to the left for underground fish or to the right for surface fish. This works because it's your fishing bobber's height, NOT your height, that determines the "depth" of your fishing. But it's YOUR biome, not your bobber's biome, that determines the fishing biome. This setup covers every possible fishing quest location except cloud, caverns, and ocean (I have teleporters to each in by base).
The full build:
My .wld file:
drive.google.com
FOR A VERSION WITH BOTH CORRUPTION AND CRIMSON, I made one here (but haven't made a build guide yet): MASTER.wld
So it's kind of like a Venn Diagram, on each platform your biome detection radius will contain ALL of the blocks for the desired biome, and only SOME of the blocks for the other biomes. For a more technical breakdown, see PapaBear's excellent showcase on this topic.
WARNING: This is pretty unforgiving, if anything is off by even one block it might break the whole farm. Please follow the directions carefully!
WARNING#2: DO NOT BUILD THIS NEAR THE OCEAN, biome detection works differently near the ocean and it tends to break artificial biomes. It's not clear why...
Step 0: Gather materials. You'll need 1500 sand, 1500 snow, 240 mud, at least 2 jungle grass seeds, at least 2 mushroom grass seeds, 125 hallowed bricks (can be added later if you're pre-wall), and 432 crimson or corruption depending on what world you got. You'll also need 176 glass and a whole lot of platforms.
Step 1: Dig down to "Level Surface", which is the border between the surface and the underground (use a depth meter if you're not sure where this is). If you want to see the background like in the GIF I posted, you'll need to use a hammer to break the natural background. NOTE: I suggest building this off to the side of your "hellevator". You'll need to dig 90 blocks sideways from your hellevator, at Level Surface.
Step 2: Place the 7 platforms as shown in the finished farm. The bottom row should be at 4' Surface, the second row at 12' Surface, and the top platform at 20' Surface. Each platform is 3 blocks wide, and there are 3 spaces vertically between each row. From here on out, I'll call your bottom-middle platform the "center platform".
Step 3: Build the pools. They need to contain 300 blocks of liquid, the size and shape don't really matter as long as the surface is at the correct height. Mine are 17 wide by 20 tall (for the underground pools)or 21 tall (for the surface pools). If you're not comfortable changing the dimensions, just copy mine. Start by placing 22 glass blocks directly below the middle of the central platform.
Then add 17 platforms to the right of the top glass block, and 17 platforms to the left of the SECOND from the top glass block.
Square up each pool by adding 18 glass blocks to the left and right of the bottom of the pillar, then building up.
Repeat this for the honey and lava pools - again 17 platforms wide and 20 or 21 bricks tall. (NOTE: don't use glass platforms for the lava pool, use hell brick or anything else immune to lava).
THE HEIGHT OF LAVA/HONEY DOES NOT MATTER, so you can build these wherever you want, I did it to the side of the existing pools just for aesthetics.
When you stand on the two lower pools, your height should be "Level Surface". When you stand on the higher two pools, your height should be "2' Surface".
Step 4: Dig, dig, dig! This is where things get tedious. From your center platform, you need to dig out an area 75 blocks above, 67 blocks below, 90 blocks to the left, and 90 blocks to the right of the central platform. I had my server of 6 folks all work together and we knocked it out in no time. If you want to go really crazy, fill the whole thing with glass walls so nothing can spawn in your farm. This took me FOREVER, so it's not for the faint of heart.
Now fill the pools! I recommend filling each pool until it overflows, just to make sure it's completely full. It's important that the two water pools be COMPLETELY full or the surface of the water won't be at the right height. Use the water duplication glitch to save time, it works for lava and honey too.
Imgur
Step 5: The snow chunk. Starting from the edge of the bottom left platform, build 33 blocks left and then 29 blocks down (double-counting the corner, meaning the corner block counts towards both your length and your width... so you're using 61 blocks to make this). I recommend you use a ruler to be certain you got it right, it should say "33x29" when highlighted. Place a single platform at the bottom.
Imgur
Imgur
From here, place a single block of snow. This block will become the top-right corner of your chunk of 1500 snow blocks, which should measure 30 blocks high by 50 blocks wide. Surround this chunk with platforms and it's done for now. TO HELP YOURSELF WITH THE NEXT STEP, extend the bottom platform (the one below the snow) all the way to the right of your giant square. That way the sand blocks have something to land on as they are placed.
Imgur
Step 6: The sand chunk. Same process as snow but mirrored. You'll build 33x29 to the right of the bottom-right platform, then place a platform just like before.
Imgur
If you extended your platform over from the underside of the snow chunk, you'll already have something for the sand to sit on. Make your 30 tall by 50 wide chunk of sand, same as you did with snow. Again, surround it with platforms to stop junk from growing.
Imgur
Step 7: The mushroom chunk. This time we're measuring from the left side of the upper-left platform. Build 33 blocks left, then 59 blocks up (again double-counting the corner for a total of 91 blocks) and place a platform at the end.
Imgur
Next we need 100 mud blocks for the mushroom biome. We're trying to get mushroom grass, which cannot grow on a block that is surrounded on all sides by mud, so we're using a row of mud 2-blocks thick in order to expose each block of mud to the air. Make the chunk of mud 50 blocks long by 2 blocks high, with the bottom-right block resting on the single platform.
Imgur
Plant at least one mushroom grass seed in the chunk, and let them spread. DO NOT place platforms around the mud until the mushroom grass has grown everywhere - the platforms can prevent mushroom grass from growing. When the grass has grown everywhere, you do need to surround the mud with platforms to prevent things from growing.
Imgur
Step 8: The jungle chunk. Measuring from the right side of the upper-right platform, this time we're going 13 blocks right then 59 blocks up (double-counting corners as usual, total of 71 blocks used for this), and again placing a platform at the end. Your mushroom chunk should be at the same height as your jungle chunk!
Imgur
Now again we'll need a chunk of mud 2-blocks thick to expose each block to air, but this time it'll be 70 blocks long for a total of 140 mud blocks used.
Imgur
Just like with the mushroom, next we plant at least one jungle grass seed then wait for it to spread everywhere. DO NOT PLACE THE PLATFORMS AROUND THE MUD UNTIL THE JUNGLE GRASS FINISHES SPREADING. But do make sure to place those platforms. It's important. I swear.
Imgur
Step 9: The hallow chunk (if you're pre-wall and have no hallow yet, just use something non-corruptable like ash as a placeholder). Starting from the top-middle platform, build 55 blocks straight up. NO PLATFORM THIS TIME, corruption/crimson and hallow won't grow anything we need to worry about.
Imgur
Once you're 55 blocks up, build a chunk of pearlstone 25 blocks wide, and 5 blocks tall, centered on the pillar you just made.
Imgur
Step 10: Corruption or Crimson (whichever you have in your world): Build a chunk directly above the Hallow chunk, this time 144 blocks wide and 3 tall, "centered" on the middle of the farm (it's an even number so you cant center it exactly in the middle, but that's OK... for this one you can be off to the left or right by a couple bricks and it won't matter. The height DOES matter.)
Imgur
Imgur
If everything went correctly, there should be a 3-block air gap between the corruption/crimson chunk and your jungle chunck / mushroom chunk (to prevent spread). Make sure everything lines up!
Step 11: THE COMPLICATED PART. We're almost done. This step adds a left and right boundary to each biome, and prevents them from overlapping with each other. Don't sweat the technical details here, just follow the instructions.
First, from the snow chunk, place 8 torches on the top platform (as a guide) starting at the top left. Then dig out a single snow block.
Imgur
Now do the same, but mirrored, to the sand chunk.
Imgur
Now we're going to put that single snow block into the hole in the sand chunk
Imgur
...and put that single sand block into the hole in the snow chunk
Imgur
Now, above the single sand block and above the single snow block, place a mud block. Plant a JUNGLE seed above the single sand block (in the snow chunk), and plant a MUSHROOM seed above the single snow block (in the sand chunk). Use the pics! As always, we also need to place a platform over the mud blocks to stop stuff from spawning.
Imgur
Imgur
Step 12: The last bounding blocks. Remove the 2 innermost torches from above the snow and sand chunks, you should now have a row of 6 torches. Above the innermost torch, build two platforms up, then place a single hallowed block. Repeat on each side. Again, use the pics as your guide!
Imgur
Imgur
Step 13: The final step! We need to remove ONE block from the mushroom chunk, ONE block from the jungle chunk, and TWO blocks from the hallow chunk. It does not matter which block, I just remove one from the corner. Copy the pics if you're not sure which one you want to remove. Also, be sure to move the platforms in the mushroom and jungle chunks as needed.
Imgur
Imgur
Imgur
Step 14: You're done! I like to decorate the 7 platforms with backgrounds to show what biomes they are, but you do whatever you like. Maybe add teleporters to the caverns, sky lake, and ocean? (that definitely helps). Build the fisherman a house next to the farm? Do whatever! Just be sure to test the platforms to make sure the background changes as you move from platform to platform. The background transition might be a bit laggy, so be patient. If something isn't working, bust out your ruler and go back to the guide, I'll bet you that something is off by just a block or two. PLEASE double-check your farm against my .wld file if you're having trouble. I've used my farm to complete every fishing quest out there so I know it works (as of 14.0.5 at least).
I'm skipping over most of the technical details because I'd end up writing a book to describe it all, like how the middle biomes actually start exactly one block above the platform below them in order to allow the 3-block airgap around evil chunks to prevent the crimson and hallow from spreading, or how the shape of each biome chunk doesn't actually matter as long as the outermost edges stay on the same vertical and horizontal planes, etc. If anyone cares to understand that stuff please hit me up, I'd be happy to discuss.
Anyway, I hope this covers everything and I hope you enjoy!
EDIT 6/7: Fixed a typo I made with the required number of crimson bricks (i put 142x3 instead of 144x3), the pictures were correct but I typed the wrong length. Sorry!
EDIT 6/8: Changed my username from Off by 1 (which was just a joke referencing my experience designing the fishing farm) to Beartopus (the name I've been using in Terraria since forever). Sorry for any confusion that causes
EDIT 6/24: For those of you who wanted a version with both corruption and crimson, I got it working! Check it out here (to the right of the base): MASTER.wld
EDIT 6/25: Attaching screenshot with my notes, this is what I use to quickly re-create the farm in a new world
The idea is that you stand on a platform to select your biome, then fish to the left for underground fish or to the right for surface fish. This works because it's your fishing bobber's height, NOT your height, that determines the "depth" of your fishing. But it's YOUR biome, not your bobber's biome, that determines the fishing biome. This setup covers every possible fishing quest location except cloud, caverns, and ocean (I have teleporters to each in by base).
The full build:
My .wld file:
ENDGAME.wld

So it's kind of like a Venn Diagram, on each platform your biome detection radius will contain ALL of the blocks for the desired biome, and only SOME of the blocks for the other biomes. For a more technical breakdown, see PapaBear's excellent showcase on this topic.
WARNING: This is pretty unforgiving, if anything is off by even one block it might break the whole farm. Please follow the directions carefully!
WARNING#2: DO NOT BUILD THIS NEAR THE OCEAN, biome detection works differently near the ocean and it tends to break artificial biomes. It's not clear why...
Step 0: Gather materials. You'll need 1500 sand, 1500 snow, 240 mud, at least 2 jungle grass seeds, at least 2 mushroom grass seeds, 125 hallowed bricks (can be added later if you're pre-wall), and 432 crimson or corruption depending on what world you got. You'll also need 176 glass and a whole lot of platforms.
Step 1: Dig down to "Level Surface", which is the border between the surface and the underground (use a depth meter if you're not sure where this is). If you want to see the background like in the GIF I posted, you'll need to use a hammer to break the natural background. NOTE: I suggest building this off to the side of your "hellevator". You'll need to dig 90 blocks sideways from your hellevator, at Level Surface.
Step 2: Place the 7 platforms as shown in the finished farm. The bottom row should be at 4' Surface, the second row at 12' Surface, and the top platform at 20' Surface. Each platform is 3 blocks wide, and there are 3 spaces vertically between each row. From here on out, I'll call your bottom-middle platform the "center platform".
Step 3: Build the pools. They need to contain 300 blocks of liquid, the size and shape don't really matter as long as the surface is at the correct height. Mine are 17 wide by 20 tall (for the underground pools)or 21 tall (for the surface pools). If you're not comfortable changing the dimensions, just copy mine. Start by placing 22 glass blocks directly below the middle of the central platform.
Then add 17 platforms to the right of the top glass block, and 17 platforms to the left of the SECOND from the top glass block.
Square up each pool by adding 18 glass blocks to the left and right of the bottom of the pillar, then building up.
Repeat this for the honey and lava pools - again 17 platforms wide and 20 or 21 bricks tall. (NOTE: don't use glass platforms for the lava pool, use hell brick or anything else immune to lava).
THE HEIGHT OF LAVA/HONEY DOES NOT MATTER, so you can build these wherever you want, I did it to the side of the existing pools just for aesthetics.
When you stand on the two lower pools, your height should be "Level Surface". When you stand on the higher two pools, your height should be "2' Surface".
Step 4: Dig, dig, dig! This is where things get tedious. From your center platform, you need to dig out an area 75 blocks above, 67 blocks below, 90 blocks to the left, and 90 blocks to the right of the central platform. I had my server of 6 folks all work together and we knocked it out in no time. If you want to go really crazy, fill the whole thing with glass walls so nothing can spawn in your farm. This took me FOREVER, so it's not for the faint of heart.
Now fill the pools! I recommend filling each pool until it overflows, just to make sure it's completely full. It's important that the two water pools be COMPLETELY full or the surface of the water won't be at the right height. Use the water duplication glitch to save time, it works for lava and honey too.
Imgur
Step 5: The snow chunk. Starting from the edge of the bottom left platform, build 33 blocks left and then 29 blocks down (double-counting the corner, meaning the corner block counts towards both your length and your width... so you're using 61 blocks to make this). I recommend you use a ruler to be certain you got it right, it should say "33x29" when highlighted. Place a single platform at the bottom.
Imgur
Imgur
From here, place a single block of snow. This block will become the top-right corner of your chunk of 1500 snow blocks, which should measure 30 blocks high by 50 blocks wide. Surround this chunk with platforms and it's done for now. TO HELP YOURSELF WITH THE NEXT STEP, extend the bottom platform (the one below the snow) all the way to the right of your giant square. That way the sand blocks have something to land on as they are placed.
Imgur
Step 6: The sand chunk. Same process as snow but mirrored. You'll build 33x29 to the right of the bottom-right platform, then place a platform just like before.
Imgur
If you extended your platform over from the underside of the snow chunk, you'll already have something for the sand to sit on. Make your 30 tall by 50 wide chunk of sand, same as you did with snow. Again, surround it with platforms to stop junk from growing.
Imgur
Step 7: The mushroom chunk. This time we're measuring from the left side of the upper-left platform. Build 33 blocks left, then 59 blocks up (again double-counting the corner for a total of 91 blocks) and place a platform at the end.
Imgur
Next we need 100 mud blocks for the mushroom biome. We're trying to get mushroom grass, which cannot grow on a block that is surrounded on all sides by mud, so we're using a row of mud 2-blocks thick in order to expose each block of mud to the air. Make the chunk of mud 50 blocks long by 2 blocks high, with the bottom-right block resting on the single platform.
Imgur
Plant at least one mushroom grass seed in the chunk, and let them spread. DO NOT place platforms around the mud until the mushroom grass has grown everywhere - the platforms can prevent mushroom grass from growing. When the grass has grown everywhere, you do need to surround the mud with platforms to prevent things from growing.
Imgur
Step 8: The jungle chunk. Measuring from the right side of the upper-right platform, this time we're going 13 blocks right then 59 blocks up (double-counting corners as usual, total of 71 blocks used for this), and again placing a platform at the end. Your mushroom chunk should be at the same height as your jungle chunk!
Imgur
Now again we'll need a chunk of mud 2-blocks thick to expose each block to air, but this time it'll be 70 blocks long for a total of 140 mud blocks used.
Imgur
Just like with the mushroom, next we plant at least one jungle grass seed then wait for it to spread everywhere. DO NOT PLACE THE PLATFORMS AROUND THE MUD UNTIL THE JUNGLE GRASS FINISHES SPREADING. But do make sure to place those platforms. It's important. I swear.
Imgur
Step 9: The hallow chunk (if you're pre-wall and have no hallow yet, just use something non-corruptable like ash as a placeholder). Starting from the top-middle platform, build 55 blocks straight up. NO PLATFORM THIS TIME, corruption/crimson and hallow won't grow anything we need to worry about.
Imgur
Once you're 55 blocks up, build a chunk of pearlstone 25 blocks wide, and 5 blocks tall, centered on the pillar you just made.
Imgur
Step 10: Corruption or Crimson (whichever you have in your world): Build a chunk directly above the Hallow chunk, this time 144 blocks wide and 3 tall, "centered" on the middle of the farm (it's an even number so you cant center it exactly in the middle, but that's OK... for this one you can be off to the left or right by a couple bricks and it won't matter. The height DOES matter.)
Imgur
Imgur
If everything went correctly, there should be a 3-block air gap between the corruption/crimson chunk and your jungle chunck / mushroom chunk (to prevent spread). Make sure everything lines up!
Step 11: THE COMPLICATED PART. We're almost done. This step adds a left and right boundary to each biome, and prevents them from overlapping with each other. Don't sweat the technical details here, just follow the instructions.
First, from the snow chunk, place 8 torches on the top platform (as a guide) starting at the top left. Then dig out a single snow block.
Imgur
Now do the same, but mirrored, to the sand chunk.
Imgur
Now we're going to put that single snow block into the hole in the sand chunk
Imgur
...and put that single sand block into the hole in the snow chunk
Imgur
Now, above the single sand block and above the single snow block, place a mud block. Plant a JUNGLE seed above the single sand block (in the snow chunk), and plant a MUSHROOM seed above the single snow block (in the sand chunk). Use the pics! As always, we also need to place a platform over the mud blocks to stop stuff from spawning.
Imgur
Imgur
Step 12: The last bounding blocks. Remove the 2 innermost torches from above the snow and sand chunks, you should now have a row of 6 torches. Above the innermost torch, build two platforms up, then place a single hallowed block. Repeat on each side. Again, use the pics as your guide!
Imgur
Imgur
Step 13: The final step! We need to remove ONE block from the mushroom chunk, ONE block from the jungle chunk, and TWO blocks from the hallow chunk. It does not matter which block, I just remove one from the corner. Copy the pics if you're not sure which one you want to remove. Also, be sure to move the platforms in the mushroom and jungle chunks as needed.
Imgur
Imgur
Imgur
Step 14: You're done! I like to decorate the 7 platforms with backgrounds to show what biomes they are, but you do whatever you like. Maybe add teleporters to the caverns, sky lake, and ocean? (that definitely helps). Build the fisherman a house next to the farm? Do whatever! Just be sure to test the platforms to make sure the background changes as you move from platform to platform. The background transition might be a bit laggy, so be patient. If something isn't working, bust out your ruler and go back to the guide, I'll bet you that something is off by just a block or two. PLEASE double-check your farm against my .wld file if you're having trouble. I've used my farm to complete every fishing quest out there so I know it works (as of 14.0.5 at least).
I'm skipping over most of the technical details because I'd end up writing a book to describe it all, like how the middle biomes actually start exactly one block above the platform below them in order to allow the 3-block airgap around evil chunks to prevent the crimson and hallow from spreading, or how the shape of each biome chunk doesn't actually matter as long as the outermost edges stay on the same vertical and horizontal planes, etc. If anyone cares to understand that stuff please hit me up, I'd be happy to discuss.
Anyway, I hope this covers everything and I hope you enjoy!
EDIT 6/7: Fixed a typo I made with the required number of crimson bricks (i put 142x3 instead of 144x3), the pictures were correct but I typed the wrong length. Sorry!
EDIT 6/8: Changed my username from Off by 1 (which was just a joke referencing my experience designing the fishing farm) to Beartopus (the name I've been using in Terraria since forever). Sorry for any confusion that causes

EDIT 6/24: For those of you who wanted a version with both corruption and crimson, I got it working! Check it out here (to the right of the base): MASTER.wld
EDIT 6/25: Attaching screenshot with my notes, this is what I use to quickly re-create the farm in a new world
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