The Call of Cthulhu isn't fantasy at all, it's pure Sci-Fi. Alien god that partially exists on a different plain of existance, is metaphysical, and abides in a city of 'impossible dimentions' = Sci-Fi. He is a 'lesser' god, not an alien, a true deity. He is on par with earth's gods who in turn answer to ancient and more powerful beings which cannot be comprehended by the mind of mankind. We are ants to Cthulhu, who is a cell to them.
I'm getting the metal image of Gandalf VS Darth Vader...
Fantasy is more 'destructive' There are beings of great power who can wipe out civilizations, some sci-fi has that (like Lovecraft's stuff), but it leans more towards Star Trek or Star Wars, spaceships and laser swords. Discounting gods and both sides, I am thinking Sci Fi. Middle Earth can have a battalion of Saurons, it doesn't amount to much when they're being turned to ash by a Death Star.