There is HomeBrew Too, right off of the LIE in queens. Main Street exit I believe. I had the equipment from my dad's wine making days. They had all the ingredients I wanted. Selection was slightly lacking, but call ahead and ask if they have what you are looking for.
Karp's homebrewing or homebrew supplies(google it), they have a website. They are about 35mi east of the city. They seem to have a wide selection, going by their website, but who knows what the actual inventory looks like. Prices actually look very good.