Purely depends on the moveset. If the Greninja has Ice Beam, then it wins, doubly so if either Sceptile's in it's Mega form or Greninja has Protean as it's ability. Ariel Ace could be a decent substitute for it as well. If it has neither move or it's up against Mega Sceptile, then things are far more in Sceptile's favour, since most of it's STAB attacks could likely oneshot Greninja as long as it can survive the first hit, even more likely due to Mega Sceptile's speed.