I read some comments from the filmmakers about this, and they say that this was pure coincidence, and they just thought the song was a good one for the scene. I think they are being honest.
The REAl question is, if the Beastie Boys exist in the Star Trek universe then how could they sing about Spock and his nerve pinch in the song “Intergalactic?” How would they know of Spock if he is “real?” My theory is that one of the Beasties was at some point on a bus in San Francisco… The same one Kirk and Spock was in Star Trek IV. He overheard them talking, saw Spock give the pinch, and filed that data away to use later…