Are you renting a car? If so, I'd stay away from downtown SF and find a place with free parking. If you have season tickets at AT&T, there will be 5 more chances to explore and stay in downtown SF if that's what you want to do. As DD, says, get an airport hotel. All the big chains have extremely cheap rates for even their nicest hotels (hyatt, marriott, westin) on the weekends. Though the nicer the hotel the higher chance you'll have to pay for things like internet and parking.
A 49er fan might have better advice here - but I'm not too impressed with the public transit options to the stadium. Cal train stops near visitacion valley and muni goes right through bayview. That might be OK because there appear to be shuttles from these stops for 49ers games, but who knows how crowded they get? there might be an easy way to get to candlestick without a car from the airport hotels, you'd likely have to find a hotel near the south san francisco or milbrae stop and walk to it. But no car means eating crappy hotel food most likely. the embassy suites that cal_fan2 recommends looks like an easy walk to caltrain, as would be the fairfield inn milbrae. Also, if it's a night game, caltrain might not have very frequent service.