The week before last, I visited the Tokyo Metropolitan Government Building in Shinjuku, which has a pair of observing decks on the 45th floor. While these aren't super high, all things considered, they do offer a pretty good view of Tokyo and some surroundings. This is probably because despite being the biggest city in the world (or biggest metropolitan area in the world, depending on your definition of "city"), Tokyo doesn't actually have a lot of really tall skyscrapers.The observing deck of the Tokyo Metropolitan Government Building is also totally free to visit. So if you have some time to kill and you're in Shinjuku and like going to the tops of tall buildings, I definitely recommend visiting it.
The Metropolitan Government Building is also pretty easy to find from Shinjuku station. If you can find your way to the area of the station with the taxi and bus stops, there are moving sidewalks from the station which will take you most of the way there underground and signage exists in English as well as Japanese indicating the path there.
