I was there a few weeks ago. Here are a few places i enjoyed.
The Blind Tiger at 281 Bleecker Street - gets very busy in the evening but is a really nice spot all the same. Huge selection of beer including a few casks.
Mugs Alehouse - 125 Bedford Avenue. Sports on tv, most beers available in 20oz as well as 16oz. the Allswell diner across the road from here is very good too.
Barcade - 388 Union Ave - great selection, lots of aracde machines.