They both have different roles, so it really does depend on the rest of your team.
If you want a fast Pokemon that can hit hard, then go with Greninja. If you want a set up sweeper, then go with Crawdaunt.
Here is a set for both of them:
Greninja @ Life Orb
EVs: 252 SAtk/252 Spd/4 Atk
- Surf/Hydro Pump
- Ice Beam
- Grass Knot/Dark Pulse/Extra Sensory
The idea is you go in, you hit the opponent hard, and then you switch out. Greninja is a very fast Pokemon. All moves get STAB because of Protean, so just choose whatever coverage you want. The last move is the reason I gave him the Hasty nature and a few EVs in attack. U-turn's main purpose isn't to damage, but to keep momentum. But if it does some alright damage at the same time, then it is better.
Crawdaunt @ Focus Sash
Jolly OR Adamant Nature
EVs: 252 Atk/252 Spd/4 HP
- Dragon Dance
- Aqua Jet
- Knock Off
Focus Sash makes sure you get a Dragon Dance off, as long as there are no entry hazards and he gets a safe switch in. At that point use your STAB attacks, which are boosted by Adaptability, to sweep. Aqua Jet is in case you aren't sure you can out speed. He gets 2 good Water STAB attacks - Crabhammer is a bit more powerful, but does have a chance to miss, which is why you might prefer Waterfall. Knock Off is a great move in Gen VI, and the boost from Adaptability makes Crawdaunt one of the best users of it.
So, as you can see, these Pokemon may share a typing, but that is about all they do share, as they are used for different things. Which one is better really does depend on your team.
I hope this helped!