From what I understand, Gengar only shines as a Mewtwo counter under two very specific circumstances.
- Mewtwo has psycho cut/focus blast
- Gengar has shadow claw (legacy)
If both criteria are met, then Gengar is pretty good as a glass cannon against Mewtwo, but only then. Mewtwo's other movesets knock Gengar out way too fast (Confusion alone tears it to pieces), and the DPS from Gengar's current two fast moves tends to be fairly mediocre. So given these limitations, that's probably why it's not recognized as a top counter.
Edit: ok, I just looked at the Mewtwo Raid Counter list, and I have to say, I'm surprised to see that mons like Umbreon (lower attack stat than Blissey) Sharpedo (nonexistent bulk) are included on the list while Gengar is not.