For Minimal Items, it's probably the last form of Ballos although I've never gotten that far. The Doctor's second form is giving me massive problems since the bats kill you in two hits and dodging the red crystal isn't as easy as it looks. On third place would be the core simply because of the massive amounts of BULLET SPAM! The Undead Core doesn't even come close to that. Monster X is tricky, too, but with proper strategy, it's easy to dodge because it's extremely pattern based.
For Maximal Items, Ballos is fairly easy. Monster X can still be a pain if it rolls over you and the missiles WILL kick your ass the first time you play through it. The Core is still annoying and the Undead Core is still easy. Surprisingly, I always found the second fight against Balrog pretty tricky because it's almost impossible to both dodge all his projectiles and still hurt him. Unless you stand on his head, of course.
Really, I don't think any boss is difficult with max items. There are a few that are annoying, but that's it.