Take this view of Tokyo Harbor. Scan around the coastline. You will notice that a vast majority of the property on the ocean is occupied by things related to:
- Manufacturing (Oil, Chemical, Petrochemical especially)
- Shipping (Warehouses, Ports, Airports, etc.)
As you can tell by the coastline, a lot of land gets created artificially to increase the amount of land that has access to the ocean, as it is in great demand for a country that does a lot of international trade, especially by ship. From Chiba to Kanagawa, the coast is virtually 100% occupied.
You can see the same thing around Kansai's Coast from Wakayama to Himeji.
Because of the demand for oceanfront property by business, something like a marina for pleasure boats is prohibitively expensive for the average person. Unlike less dense countries, there just isn't some empty land near cities to put a boat on. For pleasure craft, you are better off visiting Lake Biwa or the Japan Sea coast of Japan (which is much less densely populated), but neither will do a good job island-hopping.
The only people I have met with pleasure boats around cities in Japan are incredibly wealthy, and are unlikely to invite someone island hopping.
If you go out in to the country, specifically around the Seto Inland Sea, there are a lot more fishing villages and people with boats, and many of the islands in the Inland Sea can only be reached by boat. The same goes true for the islands between Kagoshima and Okinawa prefectures. Ferries can be infrequent, and the residents of each island can be pretty small (many have less than a thousand people).
The Seto Inland Sea is probably the best bet, as there are more islands and they are far closer together -- you are more likely to be able to find your way somewhere.
In any case, chances are you are going to need some good Japanese if you want to hitchhike on boats as you need to get outside the city. Some of these places are incredibly rural and rarely see non-residents at all, let alone non-Japanese.
If you mean sailing between major islands (like between Honshu and Kyushu, the distances tend to be greater and since there is regular ferry or train service across, it is less likely that people are going that way anyway.