If you're looking for a real Japanese restaurant, then check out Narita. This restaurant serves some of the best sushi I've had in the U.S. The California roll is really great here, and their sushi bar makes it easy to find something you like. I usually like to go here with my friends, and enjoy the long bar with its dim lighting and open counter space.
If you really want to experience the best Japanese restaurants in New York, then check out Niigata. This restaurant is housed in a former tobacco warehouse, which provides a really authentic look and feel. The sashimi is wonderful here, and it's definitely worth checking out. I also really like the fact that Niigata is located near Macy's, which adds to the authenticity.