The Pony Bar - 45th St. and 10th Ave.
They have 20, rotating, American craft brews on tap and 2 cask ales. Best part: every beer is $5 (higher alcohol beers are 8 oz. pours, most are pints.) They have great pub food, and they prominently display the last time their lines were cleaned. I've never seen a date that was more than a week ago.
Other pubs to hit up:
George Keeley's - 83rd St. and Amsterdam
Respectable beer list without a lot of macro-brews, decent food, free popcorn, darts.
Downtown Bar and Grill - Amity and Court St. in Cobble Hill, Brooklyn
Overpriced, but the dude has over 800 beers, mostly in bottles. Lots of beers that are out of season.
The Half Pint - Thompson and W. 3rd St.
Pretty large beer list, albeit padded by a lot of factory brewed lagers. Cheap, good brunch, though.
Chelsea Brewery - Pier 59, West Side Highway
Won't blow you away, but they make a few decent brews. Plus it's right on the River.
+1 on Burp Castle. That place is a trip. Small, quiet, lots of Belgian and Belgian inspired ales, and the bartender dresses like a monk. Plus Pommes Frites is right around the corner where you can get some of the best fries in NYC with like a million different dipping sauces.