Its funny, just the other day I was planning out my trip to NYC (I'm going in September) and I was looking for the same sort of stores, here's a list of the ones I found:
(Sorry if you already listed them, I'm just copying and pasting the list I made)
Everyday Beauty
163 Hester St. Chinatown, NY 10013
Kose Beauty Shop
55 Bayard St. New York, NY 10013
Daigar Beauty Shop
7 Elizabeth St. New York, NY 10013
Kan Man
2nd Floor 200 Canal St. New York, NY 10013
Kinokuniya Bookstore
1073 Ave of the Americas New York, NY 10018
Everday Beauty (There's 2 of them)
136-20 Roosevelt Ave. Ste 213 New York, NY 11354
The Face Shop (Not really gyaru, but Korean skin care products)
35 West 32nd St. Manhattan, NY 10001
The Face Shop (There's 2 of them)
136-62 39th Ave. Flushing, NY 11354
Sasa Cosmetics and Beauty
20 Pell St. Site B New York, NY 10013
Mitsuwa Marketplace
595 River Rd. Edgewater, NJ 07020 -- It's right on the border, so if you could make the effort to visit it, it'd probably be worth it.
Anna Sui
113 Greene St. Frnt. New York, NY 10012
Hope that helps you out! And happy shopping