(here goes nothing)
Ferrothorn really does a great job at countering a Greninja that doesn't have HP Fire on it (HP Fire is pretty rare in my opinion). Make sure to have Thunder Wave and Power Whip on said Ferrothorn though. Its a good combo.
These two 'mons stop every Greninja as long as the sucker doesn't have Powerup Punch. (Again, from experience, rare.)
These are pretty good counters too, but their overall usefulness for anything else is questionable.
(Hope this helped!)