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.

Tier		Attacker	Fast move	Charge move	DPS%	TDO% (Focus Blast)	TDO% (Shadow Ball)	TDO% (Hyper Beam)	TDO% (Psychic)	Comments
S (excellent)		Tyranitar	Bite	Crunch	83	40	84	100	100	"only" A-tier against Focus Blast
S (excellent)		Mewtwo	Psycho Cut	Shadow Ball	84	73	39	61	61	"only" A-tier against Shadow Ball, excellent against Focus Blast
A (good)		Gengar	any	Shadow Ball	94	50	21	46	20	Legacy Shadow Claw is best, but current moves are good too; extreme glass cannon => excellent against PC/FB and PC/HB, crap otherwise
A (good)		Houndoom	Snarl	Foul Play	81	31	48	44	57	very good against Shadow Ball and Psychic
A (good)		Tyranitar	Bite	Stone Edge	74	36	74	89	89	B-tier against Focus Blast
A (good)		Mewtwo	Confusion	Shadow Ball	80	70	37	58	58	"only" B-tier against Shadow Ball, S-tier against Focus Blast
B (decent)		Scizor	Fury Cutter	X-Scissor	77	41	36	55	43
B (decent)		Pinsir	Bug Bite or Fury Cutter	X-Scissor	79	46	33	39	30	good against Focus Blast
B (decent)		Tyranitar	Bite	Fire Blast	70	34	71	84	84	don't use against Focus Blast
B (decent)		Tyranitar	Iron Tail	Crunch	67	32	67	80	80	don't use against Focus Blast
B (decent)		Dragonite	Dragon Tail	Outrage or Dragon Claw	71	57	41	48	38
B (decent)		Houndoom	Snarl	Crunch	75	29	45	41	53	good against Shadow Ball and Psychic
C (backup)		Dragonite	Dragon Breath	Outrage	67	55	39	46	36
C (backup)		Dragonite	Dragon Tail	Dragon Pulse or Hurricane	66	54	38	45	35
C (backup)		Alakazam	Psycho Cut	Shadow Ball	75	42	22	34	34	don't use against Shadow Ball
C (backup)		Gyarados	Bite	Crunch	66	54	39	46	36	good 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.