The "Park Hyatt" hotel near Tochōmae station, Shinjuku has three restaurants with amazing panoramic views over Tokyo. I think New York Grill and Kozue are pretty high up. I've also heard that they filmed some scenes of "Lost in Translation" in the New York Grill if I'm not mistaken.
Hands down....La Sora Seed located on the 31st floor of Tokyo Solamachi with a spectacular view of Tokyo Skytree Tower. You can read more about it here on JapanTravel. http://en.japantravel.com/view/la-sora-seed-restaurant-in-tokyo
El Torito (the Mexican restaurant in California) is also a good one in Yokohama. It's on the 28th floor of Sky Building. Mexican food with a view. Nothing but awesomeness! :-)