Hi
As written above, you will mostly find pensions in Okinawa.
I went there a year and a half ago and I had a wonderful time! I can't really help you for the accommodation, as I didn't go in the same conditions (if you're traveling with your girlfriend, I guess you want something romantic on a beach).
Let me give my two cents regarding the islands:
- Miyako: very relaxing, beautiful beaches, definitely a great place to see
- Iriomote: totally awesome, but a different atmosphere (jungle, mangrove and waterfalls). I stayed at hoshinosuna pension, by the beach of the same name, you might want to consider it:
http://www.hoshinosuna.ne.jp/
- Ishigaki: didn't like it that much. The city is UGLY and although it has a couple nice spots, I don't know, I just felt it was lacking something...
- Kerama islands: only 45 minutes from Naha by boat but totally different. Great diving spots, beautiful sea, a great place to chill out
- Naha: seriously, if it's your last night and you want to do something nice, don't stay on the main island
Just my personal opinion.
You might also want to consider Taketomi island right next to Ishigaki, I didn't go there but it's famous for its traditional houses. All the other islands "only" feature the usual Japanese architecture (my only real issue with Japan), with a special "ugliness award" for the main town in Ishigaki.
Besides, if you want more details, feel free to check out my blog (signature below), I've written a post about each island I visited.
I hope you enjoy your trip to Okinawa as much as I did!