Welcome to Flyertalk.

I see you posted on another thread that you're scheduled to arrive at NRT at 4.25pm. I assume you'll be stepping off a longhaul flight and could be quite tired.

The best way that I can think of to kick off your holiday in style would be to spend the first night at a luxury hotel in Tokyo. Book a spa treatment. Splash around in the hotel pool. Have a good meal. Go to Haneda airport early the next day and catch the 6.25am flight to Ishigaki. You will be rested and relaxed and on the beach by mid-morning.

But, as the saying goes "If you're trying to get there, I wouldn't start from here."

EDITED TO ADD -- Don't forget that late Aug can mean typhoons.