On the 53rd floor of the Roppongi Hills building is the Obervatory with great views over the city. On a clear day you can see Mount Fuji. For an extra 500yen you can go up to the Sky Deck on the roof, which is worth it. It's worth getting there at least 30 mins before the sunset in case you have to queue for a ticket. (You can also reserve in advance). Blue hour when the sun has just set and the lights are coming on is the best.