The Shinjuku area has the most skyscrapers in Tokyo thanks to the area being the most seismically stable area in Tokyo and is also home to Tokyo's tallest building, the Tokyo Metropolitan Government Center (also known as Tokyo City Hall).

The Metropolitan Government Centre takes up a city block and houses 3 buildings with the main building known as Main building No.1 being a twin 48 floor tower that is split in two at the 33rd floor.

Both of the two towers house an observation deck on the 45th floor and the good thing is entry is free, the decks are generally open from 9:30 am to 5:30 pm for the south tower and 9:30 am to 11 pm for the north tower.

The Metropolitan Government Centre also houses an office of the Tokyo Tourist Information Center its located on the 1st floor and is open 7 days a week from 9:30 a.m. to 6:30 p.m excluding new year.

more info http://www.metro.tokyo.jp/ENGLISH/TMG/observat.htm