Samurott's better....by, like, a mile. No doubt in my mind that it can take Greninja. Over half of its base stats (HP, Attack, Sp. Attack, and Defense) are higher than Greninja's. Plus, it can learn Megahorn, a powerful Bug-type move, which leaves Greninja, a half-Dark type, pretty vulnerable.
EDIT: Oh, thought this was a "who would win" thing. But, yeah, that is pretty interesting. Does anyone think it might be a "theme" among Water starters? Being based on different types of warriors or warfare? Blastoise is essentially based on a tank, Feraligatr and Swampert sort of look like Sumo wrestlers, Empoleon is based on Napoleon Bonaparte and the classical Western imperialist style of war, and, as the OP already said, Samurott and Greninja fit into that theme being a samurai and ninja, respectively.