|View from Mori Tower|
Tokyo Metropolitan Government Building Observation Deck
This is the most popular of the free observations decks and it is the most accessible as most visitors end up in Shinjuku at some point. Head west from Shinjuku Station into the business area. On the way to this building you can enjoy some wonderful public sculptures and the many skyscrapers in the area.
The Tokyo Metropolitan Government Building is an incredibly large building too that is well worth viewing, I also hear there is a good cafeteria here for bargain eats that is open to the public. There is an excellent tourist information center in the building too! There is one observation deck in each of the two towers on the 45th floor and they offer some great views. The view from Tower 1 is slightly better.
Tokyo Metropolitan Government Building, 2-8-1 Nishi-Shinjuku, Shinjuku-ku, Tokyo
Bunkyo Civic Center Observation Deck
This observation deck is more off the beaten track. It isn't the tallest of observation decks but there are not that many tall buildings nearby to obstruct your view so you can see toward Shinjuku, the Metropolitan Government Building and even Mount Fuji in one photo frame. The building is unique too with the observation deck looking like a saucer embedded in a building on the 25th floor. Nearby is the Tokyo Dome and one of the prettiest Japanese Gardens, Koishikawa Korakuen (fall is pretty). The nearest train station to here is the Korakuen station on the Marunouchi and Nanboku lines.
Bunkyo-ku, Kasuga 1-16-21, Bunkyo Civic Center Bldg 25F.
Tower Hall Funabori
Definitely not on the beaten track, this small observation deck is in a tower that is only 115 meters tall, but that is still about 28 stories. You can see the Skytree to the north and Tokyo Disney to the south. It is near Funafori Station, on the north side, and it is on the Toei Shinjuku Line.
More Tokyo Highlights Posts, Shibuya Crossing, Skytree Information, etc.