I posted a video on this topic, so if you can also watch it. But I thought it would be nice to do a long post with links and pictures on all the places. Please leave a comment if you found any more shops that I don't mention.
To view the Google map I made, click here.
1073 Avenue of the Americas
This is a bookstore chain that is even in Japan. The New York City store has three floors. The basement has character goods, stationery, and children's books. The main floor has new arrivals, Japanese books and magazines. The upstairs has a Japanese traditional goods shop, a cafe, and tons of anime books, magazines, goods, etc.
13 Elizabeth Street
This is one place I really like. It has a mish-mash of assorted little shops selling figures, anime stuff, Rilakkuma, and Asian beauty stuff. The downside is that each shop has individual hours based on the seller. And its hard to catch them when they are open. A little bit hard to find--but it's there!!
595 River Rd, NJ
This place is totally worth going. It's a mini Japan to me. There's a huge Japanese grocery store complete with a bakery. It has tons of Japanese restaurants inside too. Next door, there are stores that sell books, magazines, character goods, and Japanese beauty products (a Shiseido store).
It's not in Manhattan, so you do have to take a bus. But the bus takes you directly there. Directions here!
4. New Kam Man
200 Canal Street
It is across from Little Italy and the downstairs is a grocery. The upstairs has keychains and character goods. Lots of Hello Kitty. Much of the Rilakkuma stuff is fake, but cute nevertheless. I wasn't too impressed by it, but it is in Chinatown so if you are down checking out the Elizabeth Center it's worth it to stop by.
(Various Manhattan locations)
This is a Japanese clothing department store (again that is all over Japan). They have really reasonable prices and have some great stuff. I buy tights there religiously. They have this kind called Heattech and they are so comfy and perfect for winter. Otherwise, they have cool t-shirts often with Japanese brands, Hello Kitty, and famous artists. Bo buys most of his clothes there.
There is also a small Japantown that is worth visiting. They have a couple Japanese grocery stores and some great restaurants in the area. There is also a great Japanese bakery. Otafuku is a great place for Takoyaki!! I have bought online from a place called oo35mm and I'm hearing their NYC store has lots of Japanese beauty products and cute stuff. Definitely a place I'll be checking out next time.
So that's basically the top recommendations I have. Please comment any new places or updates!