Pick one or the other, not both. I'd plump for Ishigaki: it's big enough to have plenty to do, esp. if you're into diving),and small enough to be pretty chilled out, just don't stay in the city centre. You can also daytrip to Taketomi (gorgeous!).

Getting to Ishigaki is also pretty cheap & easy for us furriners. The rack rates are indeed silly, but you can use JAL/ANA's Y10,000-anywhere-in-Japan fares direct from all of Japan's major cities, plus there are now a bunch of LCCs like Peach that fly there for <Y10k if you snag fares early enough.