I've been to NYC once or twice a year for several years while my wife has business and I get to explore. I generally download a map from beer-mapping and takes trains and walk a lot.
It's best to check the operating hours of the pubs in Brooklyn. Spuyten Duyvel has not been open when I've gotten there in the afternoon before 4, as well as Mugs Ale House (very nice, friendly bar with a good local craft selection) and Barcade. Brooklyn Brewery only gives tours on certain days and their tasting room is only open at certain times. So plan ahead before taking the train all the way to Williamsburg.
In Manhattan, my favorite bar is the Blind Tiger in the West Village. It is friendly, the food is good (and cheap for NYC), the bartenders knowledgeable and the beer selection is fantastic. I always have a nice afternoon there. Gingerman is nice, but usually very crowded. I saw several cask ales being poured at Rattle and Hum but my bartender was so inattentive that it spoiled the experience. Your results may vary.