Everything that counters Greninja cannot deal enough damage on its own to be viable on offense. Porygon2 has just barely enough Sp. Attack - Greninja has 103, but it gets to hold a Life Orb, unlike Porygon2 which needs the Eviolite or else it really isn't good. RestTalk Gyarados gets walled by pretty much anything that resists water, and Umbreon can't do anything back to Greninja.Speaking of ninja counters, one thing I've been experimenting with recently is umbreon. It's not really relevant to A and A- discussion, but it has a few interesting niches in this metagame. Sychronize allows it to get a rare toxic off on mega Sableye while resisting any and all of its relevant attacks and it counters Greninja with it's solid bulk and lack of weakness to anything Greninja runs. It's not exactly the greatest Pokemon to grace the earth, but it does have a few other niche uses as a cleric. I'd say Umbreon is D worthy while Sableye and Greninja are major threats.
4 Atk Life Orb Protean Greninja Gunk Shot vs. 252 HP / 4 Def Umbreon: 149-177 (37.8 - 44.9%) -- guaranteed 3HKO after Leftovers recovery
Its Foul Play has a 90% chance of 4HKOing it, which is nowhere near good enough. In fact, that's bad. Greninja's Gunk Shot makes it immune to Toxic, so when poison-type, Umbreon gets walled and worn down fast. Umbreon also isn't the best cleric just because it's weak to fighting and fairy, which are pretty common. Conk, Gallade, the rare Medicham, any kind of fighting priority, and then there's Alt, Diancie, Clef, and Sylveon to ruin its day as well. It'd be one thing if it were simply weak to the types and nothing else, but on top of it Umb can't really do much back to any of those bar Gallade and Medicham. It handles fightings better than fairies (it still doesn't handle fightings well period), which it can't handle at all. I'd say it's low D rank as well.