I concur about Roppongi Hills Observatory but don't forget the Big Picture too

Indeed, I second the advice that the Roppongi Hills Observatory - the night view in particular - is to be recommended. But in fact I think you can get a nice view from many other locations in the Roppongi Hills area, whether in the Roppongi Hills Mori Tower (Academy Hills) facilities on 49th floor, the higher-up lounges in the contiguous hotel and even the "ground level entrance deck" {looking to the east towards ARK Hills} offer good views of the city. Also, there is another favorite, although it may not qualify as a "building"... the Yurikamome "tram" structure linking Shimbashi with Odaiba locations; the double-decked bridge lets visitors take in the wide vista of the Port of Tokyo, without the need to go afloat. Once in Odaiba, the "beach-ish" waterfront area across from the "Big Ball" (Fuji TV Building) offers another great view.