To get a panoramic view of the Tokyo skyline, you will have to in fact leave downtown Tokyo, and this location is one of the best location to get a full view of Tokyo. See location map below.
It is a 115 meters tall free observatory close to Funabori station. With a 360 degree viewing you can see the Rainbow bridge, Mount Fuji (if the weather is good enough.), Tokyo Skytree and Tokyo Tower, Disneyland. It is a bit far from all the action in Tokyo, IMO
I used a 100 mm lens on 1.5 crop sensor for this shot. Night view here can be very interesting too.