Ferry
Use the JR Timetable for schedules and prices. You must make a reservation by phone then reconfirm at the dock at least two hours ahead of departure. If you are late, you will not get on the ferry regardless of how much in advance you phoned in the reservation. For a list of ferry routes and ferry company phone numbers, contact JNTO. (Also, please note, prices may have increased.)
To Hokkaidô: use Hachinohe or Aomori City. These are not the only places to catch a ferry but they are the most convenient. 18,000 for vehicle and driver and 1,700 per person. Use the tatami/economy class for 2,000~3,000 one way.
To Okinawa: Naha City Tourist Information Booth has a comprehensive schedule and can help you make sense of it. Tôkyô to Naha takes forty eight hours and costs 20,000~50,000. Ôsaka to Naha takes thirty four hours and costs 15,000~39,000.
There are ferries heading to Okinawa from Kôbe, Kagoshima, and most port cities. In Okinawa, it is best to use the numerous private companies. One way costs 1,700~5,500. There are also numerous ferries that run to Pusan, Singapore and other Asian cities.
For the link to JNTO and other travel sites, check out the links section.