If I am reading multiple place on the Interwebs you may be out of luck.  There were ferries running regular scheduled service from Taiwan to Okinawa but [they apparently went bankrupt][1]([OpenJourney confirms this as well][4]).

If one to believe [Wikitravel][2] there is an irregular service offered by [Star Cruises][3] but I can't confirm through their website this to be true.

[This site][5] still refers to a ferry service on a now bankrupt line but also gives a referral to [another line][6] which may provide ferry service to Okinawa from Kagoshima but that's about it.


[1]: http://www.japan-guide.com/forum/quereadisplay.html?0+53206
[2]: http://wikitravel.org/en/Okinawa
[3]: http://www.starcruises.com/en/home.aspx
[4]: http://www.openjourney.com/blogs/josh/okinawa-taiwan-ferry-48.html
[5]: http://www.japanguidebook.com/travel/getting-okinawa-70.html
[6]: http://www.rkkline.co.jp