The Pour House on 14th Street has a great selection.
I think if you're a tourist you have to hit up McSorley's. It's an old Irish pub about 7 blocks south the Pour House. It's a wild place. Like most good bars in NYC if you hit it up during happy hour or the afternoon on the weekend, it is absolutely packed. Basically they serve 2 beers: light and dark. They keep bringing them whether you want them or not. I think it's 5 bucks for 1/2 filled pints.
Another favorite is the House Of Brews on 46th and 9th. It's a bit less touristy but they've a decent selection and good atmosphere. There are a few good beer bars within 1-2 or blocks and you could spend an entire night just on one street.