Which boss is harder I feel depends on whether I'm playing Normal or Expert Mode. In Normal Mode, I don't need to prepare very much to be able to face the bosses naturally and can usually just break the Orbs/Hearts with what I have currently. The Brain of Cthulhu feels easier here since the room is a central big room that's easy to move around in, and my boomerang/magic staff equipment serves me well in defeating the Brain's minions and knocking back the Brain to keep it from hitting me. While the Eater of Worlds, is harder to summon and requires more bombs/Purification Powder to get to the Orbs, and then finding a decent spot where you can move enough before the Eater traps you in a tiny spot where you can't move at all. Getting the Vilethorn is usually a lucky incident which helps make the Eater easier, but it isn't something that can be relied on in every playthrough.
For Expert Mode the Brain feels harder than the Eater. Both bosses require much more preparation and an arena to be effective at beating them naturally. If I can get to the surface to fight the Eater with an arena I've built up there or just use Worm Food to summon it on the Corruption Surface. It makes it a manageable fight as long as I dodge the projectiles it shoots properly. While with the brain, in the 2nd stage of the fight, the mirage ability it uses makes the fight very difficult. Not only messing with my head, but when I whittle the health down very low, its very difficult for me to figure out which brain is the real one and I end up panicking when I can't tell where I'm getting damaged by one of the 4 brains. It feels like I'm trying to follow a kaleidoscope where I can't aim properly at it. Having to think in a split second where the brain teleported and reappeared.
It is for these reasons that the Eater feels harder on Normal Mode, and the Brain feels harder on Expert Mode.