Broadly speaking, accommodation on Okinawa can be divided into two brackets: cheap basic lodges, and expensive fancy resorts. Another option is sleeping in campsites.
Budget
Okinawa has a multitude of cheap minshuku-type lodges geared towards poor surfers and divers, and unlike the mainland many offer or even specialize in bed-only ç´ æ³ã¾ã; sudomari stays with no meals included. The very cheapest dorm-type places can go for less than ¥2,000, although you'll usually be looking at a minimum of ¥3,000 for your own room and around ¥5,000 if you want two meals. Watch out for hidden charges for things like air-con, fridge rental or even using the shower.
In Naha you can easily find dirt-cheap places starting from ¥1,000 per night.
Midrange
B&B-type pensions are the most common midrange option, although there are some city hotels also. Figure on around ¥10,000/person with two meals.
Top end
The other end of the spectrum is Okinawa's host of resorts, usually located on a private beach in some remote corner of the island — which means you'll be stuck eating at the resort's expensive restaurant and using their expensive watersports services. Rack rates for these places tend to be ludicrous ¥20,000+/head/night, but you can usually get steep discounts by buying flight and hotel packages, especially in the low season.