If you are staying in Ishigaki and want to go to Yaeyama islands, you can go there with a tour or buy a boat pass.
They have an “island hopping passes” for 3, 4 or 5 days. Some include Hatenma island and some do not. The price is from 5800 yen to 12,000 yen (adult).
Another company has a “Dream pass”. For a 2, 3 or 4 day pass the cost is from 3000 yen to 4500 yen (adult). It doesn’t include Hatenma island.
Please check the time tables to choose one suitable for your trip.