+1 on Mug's Ale House and Spuyten Duyvil (note correct spelling though) which are both within walking distance of the Brooklyn Brewery. Hitting all three in one day would make for a pretty sweet pub crawl. Mugs has a nice selection of taps (guessing about 30ish) and pretty decent food. Spuyten has a small tap selection, but ridiculous selection of foreign, especially Belgian bottles - not to be missed. Spuytin also has nice charcuterie and cheese to snack on, but don't expect a meal.
While you're in town you should also be sure to sample some of the other local beers Sixpoint Ales is also basesd in Brooklyn (not sure if there is a tour available) and they make some great ales including Righteous Rye, Sweet Action, and Brownstone. Look for a brown tap with a six-pointed star in any decent bar (Mugs is pretty much sure to have it). Ramstein is based in NJ and specialized in german style wheat beers, solid across the board. Kelso is also in Brooklyn and makes some nice beers, but they're very small and pretty hard to find. Captain Lawrence is just outside the city in Westchester and also makes quality beers. Bluepoint is based on Long Island, their Toasted Lager is fairly nice, but my favorite is their Dunkelweisse which might be hard to find. Obviously you already know about Brooklyn Brewery...
If you want to take beers home hit up Bierkraft in Park Slope (a neighborhood in Brooklyn) which has somewhere around 700 different beers available grouped by country/state.
In Manhattan you can try Heartland Brewery, but to be honest I think their beer is pretty forgettable and the food is bland.
New York isn't deep in brewpubs in general (real estate is just too expensive for them to make a decent go of it), but it's a great beer town overall. Check beermenus.com for events going on when you're visiting. All brands/bars above probably also have sites that you can find with a bit of googling.
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.