>>22102340First thought that comes to mind is just revenging it with scarf thunderus or something, but that's not really a "counter" per se. AV Tyranitar seems like another good way to deal with him, as he can both set up residual damage (which will help with killing it, esp if they run life orb) and can live at least one hit from a typical greninja set, unless for some reason they decide to run a physical fighting move.
Priority is also really good against him. M-Venu could probably eat him for breakfast too, unless they run extrasensory, and even then a specially defensive set will be able to tank that and then giga drain. I feel like specially defensive m-sableeye could deal with him too, WoW to make gunkshot worthless and for the residual, recover, calm mind to boost sdef and tank even more. Sturdy Magnezone can switch in on gunk shot and force him to run, Scizor can switch in on a gunkshot as well and then threaten him out with promises of banded bullet punches (just be careful for hp fire as it will OHKO). I don't know if scarfed heatran is able to outspeed max speed grenin (pretty sure he can), but if he can, you can switch in on gunk shot and then force him out with earth power. I'll try and think of some other stuff later lol.