When I 1st played Cave Story, I had some trouble with Toroko+, as well. Sitting in mostly one place while shooting the Fireball wasn't the best strategy I could've used, especially when the blocks deal -10 per hit.
Monster X definitely took the cake when it comes to the boss that I really got stuck on. There's so many shots to deal with in both phases if you don't take care of things quickly, and I even had the Bubbler (Though I didn't use it much).
Undead Core & Company came a close 2nd, however, mainly due to Frenzied Misery's Goldfish Missiles (Which I then believed to be triggered when Undead Core was nearly finished off).
On 3 Life runs, though, I'd say it's a tie between Monster X & the Regular Core. Those spinning shots are tougher than most projectiles, and sometimes my fingers just can't shoot them all down before impact.