We had a couple of hours to kill at Shinjuku Station and we'd heard you could get amazing views of the city from the nearby MetropolitanGovernment Building which has two free observation decks.
We caught the ear-popping lift to the South Observatory on the 42nd floor which had a full panoramic view. You could see all the way to the Tokyo Skytree on one side and to Mount Fuji, if it was a clear day, on the other.