Zombie brings up a good point, though. Bowser is capable of enduring some heavy firepower. His biggest disadvantage is mobility, and in that area, Ganondorf has got Bowser pretty much beat, considering he has levitation capabilities as is evidenced by Ocarina of Time.

I still have to say Bowser would take the win. He's just got a lot more abilities at his disposal, he can take enormous amounts of damage and he deals a wicked amount in return.