Does racism towards whites count? I know in modern society it doesn't much. Here's the list of stories he had racism as a major theme:
You could consider the Doom that came to Sarnath, in a way, that it has racism in it. Third world culture introduced to a highly functioning society that destroys the beautiful city of Sarnath.
The street is laden with racism towards EVERYONE, basically. The indigenous Americans, the white people that fell from grace and it's basically a love-letter to European culture that died in America.
The temple is a hate-piece against Germans.
Facts Concerning the Late Arthur Jermyn and His Family is a story about a white family's patriarch fucking a Monkey and everyone being the descendant of that race-mixing, if I recall correctly.
Herbert West–Reanimator has a stereotypically ape-like black guy.
The Lurking Fear is about a white family that turned into monsters through incest.
Rats in the walls could be considered, in a way, a racist story against whites. He writes how the elders of the white guy's family turned out to be horrible shitlords who cannibalized innocent people for god knows what reasons.
The Horror at Red Hook; need I say anything about this one?
The Call of Cthulhu has black cultists worshipping Cthulhu in the swamps.
The Very Old Folk had "hill people", I guess.
Dunwich Horror had rednecks committing acts of atrocities.
At the mountains of Madness, if you consider Shoggoths to be an allegory for blackfolk.
The thing on the doorstep could be considered as such, if you consider fishfolk to be immigrants, I guess.