In one mission in the game, Nick Fury says, "And you will know I am the DJ when I lay my beats down on you!" This is a reference to the Tarantino classic, Pulp Fiction, which featured Samuel L. Jackson (who also plays Nick Fury in the Marvel movies).
Troy Baker and Travis Willingham play brothers Loki and Thor, and also play brothers in inFAMOUS Second Son and The Crew.
The name of the 6th chapter in the game, "Red Dead Detention," is probably a nod to Rockstar's immensely popular wild west video game Red Dead Redemption.
This game has some cultural references to the Marvel Cinematic Universe.
In one mission, Dr. Octopus will climb a billboard to escape. The image present at the billboard is the cover of the first issue of Superior Spider-Man, comic that features Dr. Octopus.