I also looked into Ishigaki/Miyako Island, but it was going to cost too much.
The cheapest transport (slower ferry) to/ Zamami Island from Naha will cost 12,000yen return for the whole family. Kind of a lot for a day trip, but I'll definitely keep that in mind and may give it a go depending on the weather, any further feedback on the main island beaches, etc.
You must really get on well with your father-in-law (correct?) to plan a trip like that. That's really great.