Props for finding this.I know im not crazy but I'm sure it was in the comics... also the episode where he met the xmen he told them I'm not a mutant... I mean I dont know why I can't find proof... like it was an offhand one panel type of thing...
This comics panel does prove my point, though. He said that to 2 random people (and they still didn't believe him) lol and there's probably millions of other people who view Spider-Man as a mutant.
Also, in X-Men '97 itself, there are debates about Spider-Man's "mutant"-ness.