TL;DR: Tyranitar, Mewtwo, Gengar, Houndoom, Scizor, Pinsir, Dragonite, Alakazam, Gyarados, in this order.

Here is my personal tiered ranking of the best Mewtwo counters, including non-optimal movesets. It’s different from celandro‘s Mewtwo Raid Guide for two main reasons:

  1. My calculations are based on my Choose Your Attackers spreadsheet, which is a theoretical spreadsheet with advantages (less sensitivity to small parameter tweaks) and limitations (no breakpoints, less accuracy for specific levels). On the other hand, celandro‘s Mewtwo Raid Guide is based on Pokébattler simulations, which are harder to generalize but much more accurate for specific levels/IVs.
  2. My rankings give much more weight to DPS than to TDO/survivability, so they are more comparable to Pokébattler’s “Time to Win” rankings than to “Overall” rankings.
  3. TierAttackerFast moveCharge moveDPS%TDO% (Focus Blast)TDO% (Shadow Ball)TDO% (Hyper Beam)TDO% (Psychic)Comments
    S (excellent)TyranitarBiteCrunch834084100100"only" A-tier against Focus Blast
    S (excellent)MewtwoPsycho CutShadow Ball8473396161"only" A-tier against Shadow Ball, excellent against Focus Blast
    A (good)GengaranyShadow Ball9450214620Legacy Shadow Claw is best, but current moves are good too; extreme glass cannon => excellent against PC/FB and PC/HB, crap otherwise
    A (good)HoundoomSnarlFoul Play8131484457very good against Shadow Ball and Psychic
    A (good)TyranitarBiteStone Edge7436748989B-tier against Focus Blast
    A (good)MewtwoConfusionShadow Ball8070375858"only" B-tier against Shadow Ball, S-tier against Focus Blast
    B (decent)ScizorFury CutterX-Scissor7741365543
    B (decent)PinsirBug Bite or Fury CutterX-Scissor7946333930good against Focus Blast
    B (decent)TyranitarBiteFire Blast7034718484don't use against Focus Blast
    B (decent)TyranitarIron TailCrunch6732678080don't use against Focus Blast
    B (decent)DragoniteDragon TailOutrage or Dragon Claw7157414838
    B (decent)HoundoomSnarlCrunch7529454153good against Shadow Ball and Psychic
    C (backup)DragoniteDragon BreathOutrage6755394636
    C (backup)DragoniteDragon TailDragon Pulse or Hurricane6654384535
    C (backup)AlakazamPsycho CutShadow Ball7542223434don't use against Shadow Ball
    C (backup)GyaradosBiteCrunch6654394636good against Focus Blast

    Note: since I’m lazy, I have listed TDO based on an average of Psycho Cut and Confusion. In case of Psycho Cut, push Dark attackers a bit down and Gengar a bit up. In case of Confusion, push Dark attackers a bit up and remove Gengar completely.