Dirty Mikes, on greenwich street, The Patriot, on rector, O'haras on greenwich, and The Ginger Man on 32nd. All great bars, and you should hit them in that order. If anybody knows these places, they'll know why, and totally agree.
Unfortunately my favorite bar in Manhattan closed years ago. There used to be a bar around the block from the Beacon Theatre called Mellons. Whenever I happened into the city to go to a concert at the Beacon Theatre, I would drop in to Mellons for a couple of pints of Whatneys Red Barrel. They had a great Bartender who used to give every third pint for free. Man I miss that place.
Moonshine in Brooklyn (Columbia Street and Hamilton Ave)... Great beer selection and low key atmosphere.
Concrete on 37th St. between 8th and 9th Aves. Great for beers after work.
The Burp Castle. Small but with an incredible beer list.
Gingerman on 36th off Madison is easily my favorite. The tap selection is great. Was there the other night and they had both Fuller's London Porter and Smuttynose Barleywine Ale on tap. My boss was over from London, and we snuck out for a few, and it was his favorite bar in NYC so far, as well.