Greninja would benefit most from having Ice Beam. Mainly due to the fact that it will get STAB because of Protean (a little extra damage never hurt nobody). It'll be able to handle those pesky grass types that threaten it, knock off some flying types like Landorus, and still put out some decent damage to Pokemon that don't resist it. Using it on Mewtwo depends on which mega corn you're using. Assuming you'll be using Mewtwo Y, seeing it's more of a special attacker than it's other variant, Ice Beam will just provide better coverage for your team. If for some reason Garchomp dies and Mimikyu is unable to battle, you'll still have It to deal with those weak to ice, mainly dragon's because boy howdy there are a lot of Dragon types being used. If you do use Mega Mewtwo, then you would have to replace Mega Scizor which could cause another dilemma.
Seeing as you only have 4x weakness, ironically it's to ice, I personally say run Ice Beam on Greninja. Not only will it be STAB, but it also provides type coverage and tie that in with it's decent speed star and good Sp. Atk, it can be a good Pokemon to use