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My sister lives in NYC and my girlfriend went to school there for a bit, thus I have spent quite a bit of time down there. These are some of my favorite go to places:
Brooklyn Boulders: killer indoor bouldering and roped climbing plus slacklining and more
http://www.brooklynboulders.com/
The Longboard Loft NYC: Owned by Bustin Boards out of Brooklyn. They let you try their boards in the streets, plus they carry a bunch of other manufacturers boards and accesories.
Webster Hall: killer indie concerts (if your into that like me)
Blades: nice skateshop, a lot of sick clothing and accesories...located just above SOHO in NOHO
Uniion Square: awesome place to kill some time or spend the day, there is Paragon Sports, Wholefoods, and a shit ton of other shops...and a farmers market
Bedford Ave (and surrounding area) in Williamsburgh Brooklyn: if you havent been over before check it out, there is a ton of great restaraunts, thrift shops and random ass places to explore
I realize you already went on your trip...but I hope this helps people in the future.