Tokyoshoes has become my own person reference site. In fact the word "blog" derives from weblog, literally a log of websites. The Google can't help with things like "what is the name of that fabulous Japanese photographer girl that does these crazy self portraits." (Well, actually that search returns one of her photos in #4 under images, but that's not my point). Since I wrote about her I could easily find her name on my site. So that I can find them again, here is my list of the Japanese supermarkets in NYC near me:

M2M (55 3rd Ave btwn 10th & 11th St) - a good selection of Japanese and Korean staples.

Sunrise Mart (29 3rd Ave between 10th St & 2nd Ave) - a great place to pick up some Calpis.

Jas Mart (35 St. Marks Place btwn 2nd & 3rd Ave) - Japanese food and beauty products.