For people into Japanese culture or want to go to a place to buy Japanese products, I would suggest:
1. Bookoff on 45th street between 6th and 5th. They have Japanese games, books, manga(they even have them for $1!), and music. Of course, they're all in Japanese. So this is really helpful for those who are learning/know Japanese.
2. Kinokuniya is near Bryant Park, 6th avenue. They have a wide range of Japanese books, magazines, self-study books, and manga, of course. They also have a nice cafe on the second floor with really good food. They do have some manga and books in English.
For food/dessert, I highly suggest Pink Berry for your frozen yogurt needs. It's on Korean street, near 5th ave. The staff there are usually really nice.
Two doors down Pink Berry is a nice little Korean food court. I don't remember the name of it but next time I go there, I'll jot it down. The food there is really good for the cheap price.