Tokyo Skytree is not only the tallest tower in Japan, but also in the world. The roughly 2000 yen admission will get you to the 350 meter observation deck, where you can not only get incredible night views of the city but also stand on a glass floor and have your picture taken.
While my uncle and I only went to the tower, there are a lot of other attractions in the area like an aquarium, mall, and many restaurants. Definitely factor in enough time for the ticket line, and enjoy the vast expansiveness of Tokyo from 350 meters up.
XO,
JZ