During our visit to New York, my husband and I spent a two days and an evening in New York City. Of course, I had to find a couple of shops that carried bentos to bring back to Colorado. From my list of about five shops, I found two that were great resources, that I would highly recommend.
I like to take photos of what kinds of bentos and supplies a store offers because it's often difficult to gauge if a store is going to carry what I am in the market for. Obviously stores are going to switch up their stock, but this is what you may come to find if you visit these two locations!
494 Broome Street
New York, New York 10012
Sunrise Mart is a little gem in the West Village. When you walk in the door you'll find prepared foods, full tables of people eating, some shelves of grocery items and a real hodge podge of household goods. Go upstairs and you will find a shelf containing bentos. The selection wasn't huge, but their prices were unbeatable. I think we spent less than $5 on the bentos we purchased! Score, especially for NYC!!!
1073 Avenue of the Americas
(between 40th & 41st Sts)
New York, New York
Kinokuniya (also commonly referred to as, Kino) is directly across from Bryant Park, it can't be missed well unless you're lured in by all the fun across the street. This bookstore is a great resource for Japanese books, magazines, toys, stuffed animals, and a nice selection of bentos/houseware items. Obviously their main business is books but the selection of other items they carry is top notch! Go down the stairs to the lower level and you will find a wonderful table chock full of bentos sitting in plain view.
As far as the bento selection, their accessories are wonderful. Tons of picks, little containers, bags, elastics, and some of the nicest bentos I've seen in the states. Fair warning be prepared to pay top dollar. Their items are all Japanese imports and top of the line things, so the price matches accordingly. I went for it because bento shopping is very rare in Colorado!
Looking for more? Try Lunch In a Box, Bento Locater for shops that were submitted via readers. That's where I found these two resources, just keep in mind you may be hunting around a bit, consider it an adventure.