There are boats but if you book your flights early it is nearly the same price as taking the boat and alot faster
here is some information i found (may not be up to date)
Randy's 'Favorite Getaways in Rural Japan' -- FERRY INFO!
"There is regular ferry service from Kagoshima, at the far southern tip of Kyushu, to Okinawa. It takes 24 hours 40 minutes, leaving most evenings at 6pm. These are run by the Marix Line Co. Fares to Okinawa are ¥13,200 in second class, ¥19,200 in special second class, ¥26,400 in first class"
"# Tokyo (Ariake Pier) 4 to 7 times a month. 44-46 hours. ¥22,000-44,000
# Osaka (Nanko Pier) 4 to 7 times a month. 39 hours. ¥17,300-43,300
# Kobe (Rokko Is. Pier) 4 to 7 times a month. 43 hours. ¥17,300-43,300
# Miyazaki 4 to 6 times a month. 24 hours. ¥14,200-35,500
# Kagoshima (Honko Pier) Every other day at 6pm. 24 hours. ¥13,000-30,000. "
The ferry service through from Okinawa southwards has been cancelled so if you wanna go to Ishigaki youll have to fly! Some ferries connect the southern ilands.
A Roundtrip from Narita to Naha is around 35000yen and takes 2h30. You can book max 3 month in advance. If you collected miles with another airline you might be able to use them (i used mine i had from emirates for this flight). Book early if possible.
If you only have 3-4 days for Okinawa i´d recommend flying, otherwise youll spend 2 days (at least) on a boat. I think its worth going down there for 3 days, espcially if some can show you around. Okinawa is slightly cheaper than mainland Japan (food and rental cars). The Aquarium is nice and the war Museum is a must. They also have some nice beaches outside of naha, so think of renting a car or motobike (cars start from 2500yen a day if you are not there in golden week). Been there in April and it was warm enough to swimm but not hot yet.
Have fun