Nothing is cheap in NYC. Everything is overpriced. For cheap stuff you have to leave the city and go somewhere else.
There are some vintage clothing shops that have OK prices, like Metropolis in Astor Place and Mystery Train in Williamsburg.
In Williamsburg there are a couple places that might have something good, but they get picked through so often that you never know what you'll find. Beacon's Closet and Buffalo Exchange are really well known second hand clothing shops. Walking down and around Bedford Ave there are random clothing shops. I actually hate shopping for clothes, so I do it once a year and it's usually on the internet, so I'm not an expert on it.
There are some really great vintage clothing shops that carry really cool shit, but the prices are insane.
Maybe someone else on here knows of more places to check out.