These were provided by a co-worker of my wife, who lived in Japan for years. All descriptions were his. Not trying to take credit, just don't want to violate his privacy w/o his permission (he's a lawyer)!
Your progress on this list (you can make more progress by trying out restaurants on this list!)
Not really a Japanese restaurant per se, but a three-course dessert restaurant run by a Japanese chef who prepares the desserts in front of you in a very dainty Japanese way. If you can’t wait on the long line always in front of this place, she also has a dessert takeaway place across the street. Great date spot or place to impress people from out of town with how cool New York is.
I only add this in because it is the only authentic Japanese restaurant in the Wall Street area, and better than the other Japanese options around here. The sushi is reasonably good. The mid-town location is more like a real izakaya and has better food, especially the (extremely) spicy ramen, which is only made in limited batches, so you have to get there early to get any. Sano-san, who owns Taro Sushi, started at Ise, but I am not sure which branch.
Perhaps my favorite ramen place in New York. Ippudo is better known, but it’s a “scene” and you have to wait forever to get seated. The ramen in the two places is about the same quality, but Minca has a much more authentic atmosphere.
is an izakaya that attracts a lot of Japanese businesspeople in midtown, with a bar on the second floor where only Japanese salarymen and the occasional Japanese-speaking American go. They serve food until 2:00 am. I had many very late nights here when I worked in midtown. They have really great kara-age (Japanese fried chicken).
is another yakitori/izakaya place. The food here is really good and it’s surprisingly cheap, but because it’s cheap they depend on high turnover and they try to rush you out. But the food is good, and this place was actually featured in Anthony Bourdain’s show, “No Reservations.”
is another place, like Soba Totto, where they make soba noodles by hand. Located in the East Village, but away from the strip on St. Mark’s. Too expensive for the NYU student crowd for the most part. This may be my wife’s favorite Japanese restaurant in the city, at least until she discovered Hibino and Kappa Sake House.