I made Korea Japan by boat... Well, you 'll just have to work for one night, so it's pretty cool! But from the US, I'm pretty sure the Pacific Float needs some volunteers, and there must be some tactician exercises not far from Hawaii and thus maybe the Oganasewara Islands, 1500 km far from Tokyo, but belonging to Tokyo prefecture. From Ferry to ferry, then you'll make your way to Japan!
Another way is from China, maybe you could first go to China, and then embark on a boat from Shangai to Japan, which is pretty common, daily I would say. Check with merchandise boat, or postal boat...
Have a good trip!