Water Shuriken is bad in all its forms. Its max power is 75 (which is very rare, as in 15% of the time) and it can go as low as 30 BP, which is never good. You're better of using Surf or Scald, as they give reliable power and Scald also has a nice chance of burning. You're better off using a Z-Move, Scarf/Specs of Life Orb set, as First Sinner said. :
Here's a moveset for Protean Greninja, courtesy Smogon
Greninja @ Waterium Z
Ability: Protean
Hasty Nature
4 Atk/252 SpA/252 Spe
- Hydro Pump
- Gunk Shot/Ice Beam
- Hidden Power (Fire)
- Spikes/U - Turn