The November issue of Wine Enthusiast has an article about wine bars in New York City. I confess that I do not know much about wine bars in NYC, so i can't vouch for the choices in the article, but it looks like a pretty good beginner's guide.
I like the fact that the write breaks the bars down by the regions the bars specialize in and he does a good job of describing the atmosphere in a concise fashion:
Thirty three seats arranged around an intimate oval bar make this West Village locale an excellent choice for meeting old friends or making new ones. The wood-topped bar, with its frosted glass base encased in delicate ironwork, sits beneath hanging Riedel glassware of all shapes and sizes.
That description is of Lelabar, which does sound/look really cool :).
One thing that disappointed me was the lack of mention of any wine bars that specialize in wines from New York, or that at least have a good selection from New York.