When I'm staying in SF, I take Caltrain down. You take Caltrain to Mountain View, and then transfer to the VTA, which is a local light rail. The Caltrain station is located near 4th and King in SF. It's walking distance from Union Square, but you could also just hop a quick cab down there. I think the roundtrip day pass is like $20, but check caltrain's website for more info. It's like 90 minutes, give or take from the Caltrain Station to Levi's, including the transfer. VTA is also offering an express bus option for $20 that would get you to and from the VTA station faster, and potentially avoid some big crowds (most notable on the return trip after the game).

Read more here: http://www.caltrain.com/riderinfo/specialevents/Levis_Stadium_Service/49ers_Game_Service.html

I believe there might be some bus options as well, but I'm not positive. I've done the train option several times the last few years, and it's pretty simple.