EvolutionOfStyle.com
Well, this isn't in NYC, but it is run by my friends Jonathan and Randall and is pretty great.
Lounge: 593 Broadway @ Houston
Lots of wild clothing and shoes. Ask for Luis and tell him Christian/Jonathan sent you. He usually works until 5:00 PM.
Atrium: 644 Broadway @ Bleeker
Similarly wild clothing and shoes.
Ari: 471 West Broadway @ Houston
Very upscale, somewhere between trendy and classy. Not cheap, but beautiful stuff.
EOS: 259 Bleeker @ Cornelia
Inexpensive but awesome watches and sunglasses
Visions of Tibet: 167 Thompson St @ Houston
Lots of inexpensive tibetan/buddhist rings, bracelets, etc.
Bruno Cucinelli: 359 Bleeker @ Charles
Ridiculously expensive, but unparalleled Italian clothing
Scoop: 473 Broadway @ Broome
Cool and trendy, not too overpriced.
Jump: 89 Spring Street @ Broadway
Hip and trendy shoes.
Tokio7: 64 East 7th @ 1st
Consignment shopping at its best.
Odin: 199 Lafayette @ Broome
Trendy and very unique stuff. Great jewelry.
St. Mark's Street
There are several thrift stores on St. Mark's with unique stuff.
Paul Smith: 142 Greene Street @ Houston
Very expensive but beautiful and quirky designer.
Paramount Costumes: 52 W 29th and 6th Ave
Great costumes, masks and other fun toys