Blastoise. As mentioned above, Bowser's fire would be ineffective against Blastoise and Bowser can't even beat a midget plumber in a fight.
You guys are focusing too much on the fire. Bowser has claws, hammers, nimble jumping, and a spiked shell. Blastoise is slow, immobile, and his hydro cannons are his only meaningful weapon.
As for the Mario argument, it's not a worthy comparison. Mario is more nimble and tactically intelligent than both Blastoise and Bowser. Blastoise is less nimble and intelligent than Bowser. Mario beats Bowser because of advantages Blastoise doesn't have, so there's no reason to bring him into this conversation.