Tokyo offers a number of different free observation decks with good panoramic views of the city: the Tokyo Metropolitan Government Building in Shinjuku is one of them.
At 243 meters in height it used to be the tallest building in Tokyo, until it was overtaken by Midtown Tower in 2007. The building has two towers, and each houses a 45th-floor observatory at a height of 202 meters, which you can reach in an elevator that takes only 55 seconds. Both towers offer an amazing view of the city and on clear days you can even see as far as Mount Fuji. Both observation decks have a cafè, and the one in the North Tower also has a souvenir shop.
The North Observatory is open from 9.30am until 11.00pm, and is closed on the 2nd and 4th Mondays of each month. The South Observatory opens at 9.30am and closes at 5.30pm, and is closed on the 1st and 3rd Tuesdays of the month.