As Japan consist of many islands, it is no wander that ferries had taken a major role of transportation between islands until bullet train emerged.
While some of the routs discontinued anymore, many have worked for carrying containers, vehicles and passenger.
Ferry companies earn most of their profit from cargos, but they devote their passion for passenger comfort. Some of latest ferries have good restaurants, movie theaters, KARAOKE rooms, spas. In the mean time old-style ferries have no restaurant or entertainment facilities. In case there are no choice other than old-style ones in your route, you don’t have to worry, there are bunch of vending machines, including frozen meals, pot noodles, and beers. That should be fun.
Even second class cabin has become comfortable, if you pay extra money you will be able to stay in TATAMI room and sleep with FUTON.
Ferry sailing takes longer than air/land transport, but you had better know that Japanese air planes and bullet trains are always packed with passengers, so you might have much trouble with big back packs. Other than that you can save money for a stay at a hotel.