Transportation -Ferry-

There are few ferry companies in Tokyo.

Ferry to Hokkaido Area
there are several options for different destination.
those ticket is BUS + FERRY.
all Bus from Tokyo station.
option is below.
1.Tokyo⇔Sapporo
2.Tokyo⇔Otaru
3.Tokyo⇔Asahikawa
4.Tokyo⇔Furano

http://www.sunflower.co.jp/english/ferry/campaign/story/index.shtml
http://www.sunflower.co.jp/english/index.shtml

Ferry to Island in Tokyo-to
Takeshiba Passenger Ship Terminal(1-16-3 Kaigan Minato-ku Tokyo)
1.Miyake-jima,Mikura-jima,Hachijo-jima
2.Oo-shima,Tone-jima,Nii-jima,Shikine-jima,Kouzu-shima
3.Chichi-jima(http://www.ogasawarakaiun.co.jp/english/)

http://www.tptc.co.jp/en/tarminal/tabid/1502/Default.aspx

Ferry to Tokushima and Northan Kyushu
Tokyo Port Ferry Terminal(4-8-6 Ariake Koto-ku Tokyo)

http://www.otf.jp/fee/(only in Japanese)

Ferry to Southern Kyushu and Okinawa Area
Ariake Passenger Ship Terminal(4-7-1 Ariake Koto-ku Tokyo)

http://www.aline-ferry.com/toukyou/time.html#(only in Japanese)