I've seen elsewhere on an EA forum that each team is sent a letter asking permission to use their arena's name and likeness. If that document isn't signed/sent back to EA, they don't put it in the game. It's been suggested that because of the transformation at MSG, the owners haven't done so because they don't want the likeness of the arena used until all phases of the transformation is complete. That would explain why in NBA Live, MSG agreed to EA's request to use the naming rights, but not for the NHL game.
NBA 2K also hasn't been able to use MSG's name in its game as well.
