Many city skylines (e.g. Hong Kong) are best viewed from the city's harbour. In Tokyo's case, the harbour front (Tokyo Bay) is mostly industrial areas, logistical operations and warehouses. There's a great view: but not necessarily the best.
There are 5 good spots to view Tokyo.
1. Tokyo Skytree (opened May 2012)Tokyo Skytree is the World's second tallest structure at 634m (2 080 feet). The entrance fees are a little steep (currently 3000 yen). However, with observation decks at 350 m (1,150 ft) and 450 m (1,480 ft) there's nothing that compares.
2. Tokyo City HallThe Tokyo Metropolitan Government Building (also known as Tokyo City Hall) has two panoramic observation decks that are 202 meters high (45th floor). The best thing: they're free and open until 23:00 on weekdays. Photography is permitted but tripods aren't allowed.
Tokyo City Hall is located in Shinjuku (Tokyo's largest neighborhood). The nighttime view from the building is stunning.
3. OdaibaOdaiba is a multi-trillion yen artificial island in Tokyo Bay. It's a popular spot for tourists. It's also known amongst young Tokyoites as a good spot for a date. The area features countless attractions, shops and restaurants. There's also a decent view of Tokyo.
4. Tokyo TowerThe classic view of Tokyo open since 1958. Over 150 million people have visited the tower's two observation decks at 150 metres (490 ft) and 250 meters.
5. Roppongi HillsRoppongi Hills is an upscale 54 storey office and residential complex in Roppongi. It has a modern art museum on the 53rd floor (Mori Art Museum) and a panoramic observation deck. The building also features a confusing maze (there's a urban legend that the building was intentionally constructed as a maze) of shops, restaurants, spas and a large movie theatre.
(view from Roppongi Hills)