A list of highly recommended boutiques and spots to hit for funky and awesome clothing in NYC:

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