These aren't brew pubs, but they are great places to get beer in NYC:
Loreley (
http://www.loreleynyc.com/): German restaurant/beer garden. They have a lot of delicious German beer, on tap - Kolsch, Schwarzbeir, Hefewizen, lots of Pilsners - and even more in the bottle. If you are interested at all in German beers, here's a good place to try many varieties. Foods good, too. Sit out back.
Taproom 307 (
http://www.taproom307.com/): Basically a neighborhood bar, but with an enormous rotating group of great craft beers on tap. They tend to have a lot of local stuff (Kelso, Coney Island, Sixpoint), so if you want to drink local, they're good. Foods not bad either. FYI - they are a sports bar, and cater a bit to the bridge-and-tunnel crowd, so they can be busy after work. Great on weekends, though.
Blind Tiger Ale House (
http://www.blindtigeralehouse.com/): THE famous beer place in NYC - loads of stuff on tap, loads of stuff in bottles. Can be crowded and scene-y.
dba (
http://www.drinkgoodstuff.com/): Local bar on the LES with lots of beer on tap and in bottles. Haven't been in a while, but I don't remember is being super crowded.
Not a bar, but fun to visit: the Beer Room at the Bowery Whole Foods (Bowery and Houston). A CRAP TON of beer, as well as six rotating beers on tap that they sell in growlers (no drinking in the store, unfortunately), and a small amount of homebrew stuff. Lots of single bottles if you have a frig in your hotel.
And if you like bourbon, I recommend Char No 4 in Brooklyn - a couple of stops in on the F, and they smoke their own bacon in house. Delicious!