So far, two other universes have been announced, the classic Amazing Spider-Man universe, featuring Kraven the Hunter as the main boss, and the Noir Spider-Man universe, which will feature Hammerhead and the Goblin as bosses. The 2099 universe will feature a robotic Hobgoblin as the main boss.
The character of Spider-Man 2099 originated in 1992 as a possible future for the current universe. The series last for 46 issues until it was canceled in 1996. The series, which was part of a universe that featured a variety of futuristic Marvel characters, has been revisited in the comics numerous times since, but this is the first time Spider-Man 2099 will show up in a video game.
The fourth and final dimension will be revealed sometime soon, most likely around the San Diego Comic-Con. The latest trailer, which revealed the 2099 universe, hints at the last one, which looks like it could involve symbiotes or zombies.
The name Miguel O'Hara will never stop being funny to me.