The best way to counter Mega Mewtwo Y is to use Sucker Punch which will likely KO it due to its bad Defence. Since Sucker Punch will have +2 priority when Mewtwo attacks, it is basically defenceless.
Good Sucker Punch users that can defeat Mewtwo include Bisharp, Yveltal, Absol, etc. Mega Mawile is also a good counter as it learns Sucker Punch and does not take super effective damage from any of Mewtwo's common attacks. Assuming this is competitive, Yveltal is easily the best way to beat Mewtwo.