Yokohama Bay
Just south of Tokyo, about 30 minutes by train, you'll find Yokohama, the first major international port at the beginning of the Meiji period in Japan. You will definitely find yourself spending at least a day or two in Yokohama during your time in Tokyo, so it is a great place to get a little bit of seafaring in.
The terminal is in Sakuragicho, Yokohama, also called "Minato Mirai (future port), and is a bustling modern district on the cutting edge of city planning and technology. You have a couple of options for a cruise: the more luxurious cruise boat with dinner, or the shorter and less expensive "Sea Bass" to take you along for a quick ride on the coast.
http://www.yokohama-cruising.jp/html/pdf/pamphlet_english.pdf
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