Sorry, I have not been there, but my friend highly recommends this hotel. The hotel is very quiet and the hotel staffs are very nice (he said). From Ishigaki airport, it takes 30 mins by cab and the hotel is located bits far from downtown. The problem is that dinner at the hotel restaurants are expensive.
http://www.seamensclub.co.jp/index.htm
Otherwise, ANA hotel ?
http://www.anaisg.com/