If you decide to go with a special attacking set, your best options are Grass Knot, Extrasensory, Dark Pulse and Surf/Scald. Blizzard was also an option in the previous version, but the TM was removed in the current version. Greninja's best physical attacks that are available at this point are Waterfall, Night Slash, Rock Slide and Acrobatics.
A pure special attacking set is in my opinion superior, also because of Greninja's higher Special Attack stat. If you still prefer a mixed set, you could include Rock Slide and/or Acrobatics in its moveset for some extra coverage.