For me it would be:
3. Gohma (Ocarina of Time- Inside Deku Tree)- Simple. shoot the eye and keep stabbing it.
2. Gohma (Wind Waker- Dragon Roost Cavern)- Once you know what to do, you really can't be harmed by him.
1. Fyrus (Twilight Princess- Goron Mines)- The first time I fought him, I never got hit once. Its the easiest boss, even though he's huge. Only one phase, too.
Seems like the fire dungeons have the easier bosses for some reason.

