There are a ton of Sports Bars in NYC, but NYC isn't much of a college football town, September is still baseball season in NYC. The best thing to do is grab a paper when you get up there and check the sports section.
If don't care about atmosphere and the game is on ESPN, the ESPNZONE in Times Square is a decent place to watch a game, Its pretty commercial, but they have the best screens to watch the game on, and you might see some sports celebrities there.