A short walk from Shinjuku Station, visit the Tokyo Metropolitan Government Office Building, home to the Tokyo Metropolitan Government. Less famous than its cousins the Tokyo Tower and the Tokyo Skytree, the building's twin towers each have an observation deck located at the whopping height of 202 meters. Better yet, they're completely free to visit.
The Tokyo Metropolitan Government Office Building's upper floors are split across two towers, a north tower and a south tower. Each has an observation deck on the 45th floor. The South Tower is better for daytime views as you can see all the way to Odaiba in Tokyo Bay. Open until 10.30 p.m., the North Tower is better for nighttime views and is home to a bar and a cafe.
From the towers, you can see Tokyo landmarks such as Tokyo Skytree, Tokyo Tower, Tokyo Bay, and sometimes as far as Mt. Fuji. Around the edge of the observation deck, maps point out significant points that can be seen from the towers.
The best views can be had in the early morning in autumn and winter, as the air is cooler and less hazy.
In each observation deck is a gift shop selling Tokyo souvenirs, making the towers the perfect destination if you've only got time to visit one place in Tokyo and need to prove you've been there.
On certain days you may find a local produce fair in the lobby of the building. If you're lucky enough for the fair to be on while you're there, make sure to head down to sample produce from the more regional parts of Japan.