Sora House
Inexpensive, friendly hostel. Right next to monorail station and 24-hr grocery store. The staff only speaks a bit of English, but they are very friendly and helpful. The staff can help to arrange trips around Okinawa. If you get a chance to attend to one, you probably should.
Hotel Marine West Naha
A business hotel that is suitable for divers. It has drying space for scuba diving gear and free parking. There is free internet. Room prices include Japanese breakfast. Staff are friendly, though they only speak Japanese.
Naha's budget accommodations are famously cheap, but you tend to get what you pay for and some can be incredibly dirty.
Grace Naha Hotel
Small family-run guest house. Inexpensive, incredibly friendly and spotlessly clean.
Base Okinawa
Ten dorm rooms and a couple of lounge rooms make this a really nice place to stay when on a budget. There is also free Internet, laundry, bikes, etc. If you want to get there, walk up the street from the Kencho-mae monorail station towards Wakasa. After passing Wakasa-dori, turn left at the first crossing without a traffic light there's a very small sign there that says "BASE".