https://youtube.com/watch?v=xXt0ZHzQ...lzc2lvbg%3D%3D
In this mission, Spider-Man has no clue where the Spider-Bots come from, even though if he had multiversal experience, this should have reminded him of it.
I still consider them canon since they are not OUTRIGHT condradicted and were mostly written by one of the writers for the first game, giving them some level of legitimacy. Plus, the earth designation 1048 given in the comics was referenced in Insomniac Wolverine trailer.
The only comic that I think is most likely non-canon is Spider-Man Velocity, since it was written by someone with no involvement in the games and its portrayal seemed to condradict Mysterio's portrayal in the game, but I need to look up Mysterio side mission to be 100% sure.
ATSV appearance probably takes place after the second game, at least going by Peter's version of the scene in the game in the above Youtube link.