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The most in-demand place to take in the view right now is Tokyo Skytree, the tallest tower in the world. The futuristic glass tower and the shopping area surrounding it turn a year old in May 2013. The complex can see more than a million visitors over holiday periods. Plan to reserve your tickets in advance for busy days!
Before the Skytree replaced it as a broadcast beacon, the orange and white Tokyo Tower had been the tourist tower of choice since it opened in 1958. The attractions in the lower floors, including a wax museum, could be described as a bit retro. Unlike the Skytree, you have the option of walking up the 531 steps to the top, and getting a certificate to prove it.
Right in the middle of the Shinjuku “skyscraper district” is the Tokyo Metropolitan Government building, known in Japanese as the Tocho, or City Hall. The observation deck is free. There are signs in Shinjuku station to point you in the right direction - but if you get lost outside, just look for the building’s distinctive double towers. There is tourist information in several languages in the elevator lobby. There is also a cafe at the top that sometimes has live piano music.
The best option for getting a dose of culture with your view is the open-air roofdeck of the Mori Tower in Roppongi. The ticket includes admission to the Mori Art Museum a few floors below, which hosts contemporary art shows by well known international and Japanese artists. At the top, staff will snap a digital souvenir picture of you that you can purchase on your way out, and they will also happily take your picture for your with your own camera or cellphone for free.