Thanks to all for the comments from previous trips. Just got back from 4 great nights in NYC (followed by Portsmouth, New Brunswick, Portland then Vermont!).
In New York, I hit the following:
Bierkraft: good bottle lineup, neat place to have a pint out back;
Blind Tiger: very busy on a Sunday afternoon, but was a great spot with lots of interesting taps;
Swift Hibernian Lounge: just ok tap list, but you really feel like this is a great local spot while in there;
Brouwerij Lane (Brooklyn): got a heads up on this place from the bartender at Torst when he heard that my wife wanted shots of Manhattan at night. Like Bierkraft and so many other spots around town a mix of bar/bottle shop. Great tap list, lots of bottles to choose from and a super cool patio/garden out back. And just outside was a great quai to look out at Manhattan.
Brooklyn Brewery: Place was insane on a Saturday afternoon. I hate the setup of standing in line to buy tokens then standing in another line to get the beer. I wouldn't go back.
Pony Bar 10th ave: Solid tap list and great pub food. Very busy on a Friday night.
Ginger Man: not a bad tap list, pretty solid bottle list. Lively late on a Thusday night;
Rattle N Hum: loved this spot. Great tap list, bunch of kegs, solid bottles and a great liquidation rack for bottles in the back;
Top Hops Beer Shop: like Bierkraft and Brouwerij Lane, solid little tap list, decent bottle selection;
Torst: really cool spot, awesome tap selection (Pannepot on tap, yes please) and some well chosen bottles. We were in early on Saturday so it wasn't busy. Bar staff offered up some great local pointers (see above);
Whole Foods Bowery: best bottle selection/price equation I could find in NYC.
Gourmet Market: stopped in here before jumping on the Highline, I can't find it listed anywhere, but 4 great casks and another half dozen well chosen taps. Was a great spot.
There was also one other bottle/bar place I stopped in at between Pony Bar and Times square that was solid, but I forget the name.
Loved the beer scene, although I found the lack of really great bottle shops a bit bemusing. All the beer store/bar places had decent to good bottle selections, but I wasn't blown away by any. I didn't care much since I wasn't looking to carry around bottles all day, but for a city with so much of everything, I find it odd that I couldn't find a real kick-ass place to shop for bottles.