On the 25th floor of the Bunkyo-ku Civic Center is a lovely Japanese restaurant called Chinzan-so Restaurant (Civic Sky Restaurant) シビック スカイレストラン椿山荘 with spectacular views of the city. It overlooks the Tokyo Dome in the direction of Tokyo Bay; you can see the Tokyo Tower, Rainbow Bridge and Odaiba Ferris Wheel, which are especially magical when dining at night.
Meals are reasonably-priced Japanese dishes; the menu is in Japanese but there are plastic models by the door. Seating is western-style, making it comfortable for diners not used to tatami flooring. Chinzan-so Restaurant is open for lunch from 11:30 am to 4 pm and for dinner from 5 to 9:30 pm. It is open every day except May 3rd, and December 29th to January 3rd. The Bunkyo-ku Civic Center is located above the Tokyo Metro Korakuen station.
The website is only in Japanese but has some photographs: http://www.chinzanso.com/restaurant/civic/index.html