All three Pokemon are very good, so let's look at every one of them.
Greninja is available as the starter Pokemon, so you're gonna have no problem getting it. It has decent Attack and Special Attack stats with a nice Speed stat. Its Water/Dark typing is only doing Greninja favours, especially since the extra Dark-typing is not weak to any of the Gym Leaders except Valerie. It has access to a movepool diverse in types via TMs and its moveset is pretty decent as well. Has 5 weaknesses, 6 resistances and an immunity.
Blastoise is available fairly early in Lumiose, which is also highly convenient. While Blastoise appears more bulky, its access to Mega Evolution(!!!) turns him into a beast, especially in Special Attack. Its movepool is less diverse than that of Greninja's. You should use Blastoise if you a) want a bulkier Pokemon on your team or b) want a Mega Evolution. Has 2 weaknesses and 4 resistances.
Poliwrath is first available at Route 14, which is the route you go on before your fifth Gym Badge, so Poliwag isn't obtainable early on. However, if you are able to trade a Poliwag into your game early on, it might be worth your while: although Poliwrath doesn't have access to that many types, it can learn some very valuable moves early on such as Hypnosis, Body Slam and DoubleSlap. Poliwhirl and Poliwrath also have access to a few valuable Fighting-type moves in the Level 30s. Water Absorb is also a great ability compared to the Torrent ability. Furthermore, you can evolve Poliwhirl any time you want past Level 25 assuming you have a Water Stone with you. It has fairly well-rounded stats except for its Special Attack and Speed; the Special Attack can be fairly detrimental since most Water-type moves are Special. Has 5 weaknesses and 7 resistances.
I believe that Poliwrath is the best option among this selection, if you are willing to trade one into your game early on. But if you're not into that, I would choose Blastoise. And if you're not a fan of Mega Evolution and/or you prefer offense over defense (which people tend to do when creating in-game teams), Greninja is the Pokemon to use. Of course, don't rule out looking out for other Water-type alternatives, since there are plenty available in the Kalos region!
Hope I helped. :)
Source: The wonderful database of Serebii