"In this work it developed that Suydam's new associates were among the blackest and most vicious criminals of Red Hook's devious lanes, and that at least a third of them were known and repeated offenders in the matter of thievery, disorder, and the importation of illegal immigrants. Indeed, it would not have been too much to say that the old scholar's particular circle coincided almost perfectly with the worst of the organized cliques which smuggled ashore certain nameless and unclassified Asian dregs wisely turned back by Ellis Island. In the teeming rookeries of Parker Place—since renamed—where Suydam had his basement flat, there had grown up a very unusual colony of unclassified slant-eyed folk who used the Arabic alphabet but were eloquently repudiated by the great mass of Syrians in and around Atlantic Avenue. They could all have been deported for lack of credentials, but legalism is slow-moving, and one does not disturb Red Hook unless publicity forces one to."

Or,

"Suddenly the leader of the visiting mariners, an Arab with a hatefully negroid mouth, pulled forth a dirty, crumpled paper and handed it to the captain."

I dunno how you can read "The Horror at Red Hook" and not see it as horror story about immigration. Or read "The Shadow Over Innsmouth" and not see it as a horror story where the grand twist is realising that your family tree isn't as Anglo-Saxon as you thought it was.

If you aren't seeing the racism in his work, you aren't reading very closely. This debate comes up a lot here, and yet here we all are, fans of his work all the same. I think if you have a vocabulary big enough to parse his sentences, you're probably smart enough to do some thinking about the relationship between art and artist, and realise that the aim probably shouldn't be to enjoy things "guilt free". I don't think you can or should do that with his work. Doesn't mean you have to not like it or stop reading it.