For authentic Japanese, try Ise for sushi (56th st, bewteen 5th and 6th ave), Men Kui Tei for ramen (right next to Ise) and Soba Nippon for soba (52nd st, between 5th and 6th ave)
Mamafuko noodle bar is totally overrated. Their milk bar has a good selection of sweets though. If you don't mind travelling, there're tons of great Japanese restraunts in the same neighborhood. For a light dinner, try Yakitori Taisho. Their yakitori is as authentic as you can get.
I frequented Wagamama when I was travelling in Europe. Their food is not authentic, but tasty nevertheless. I'd like to see them open up a branch in NYC.