The main focus of Lovecraft's works are indeed... aliens. Lots and lots of aliens. Some visited Earth and lived on it. Some battled between themselves. Some built cities. Some destroyed cities. Some created civilizations (some of which collapsed and left ruins behind them). Some left, some are sleeping, some are well awake. Some are good, some are evil, some are neutral. Some are physical beings, some... well, not exactly.
Lovecraft was indeed one of the first writers to write about alien beings. He wrote about them so early, in fact, that "proper" sci-fi didn't even exist yet... so he was considered a horror writer; but... wouldn't you actually feel horrified if reading about hostile alien beings lurking everywhere, when nobody had yet bothered considering them a pseudo-scientific issue?
Stories like The Whisperer in the Darkness or At the Mountains of Madness don't have anything even remotely magical in them, "only" aliens; and, by the way, it is well known that "any sufficiently advanced technology can't be distinguished from magic"
So, can Lovecraft be considered a science fiction writer? Did later SF writers recognize him as a father of the genre?