The Bunkyo Civic Center is a great way to see Tokyo from above. You will be able to see Mount Fuji on clear days, the Skyscrapers of Shinjuku and Ikebukuro from its observation deck.
Like the Twin Towers of the Tokyo Metropolitan Government Building in Shinjuku the entrance at the Bunkyo Civic Center is free. The Bunkyo Civic Building is 105 meters, or 344 foot, high and has 26 stories, The observation deck is on the 25th floor and is especially good for night viewing because of the slanted position of its windows.
Their is a restaurant at the observation deck where one can enjoy a meal or a cup of coffee while viewing the sights.
The center is open from 09:00 am to 08:30 pm. The entrance is free of charge.