Kayaking is a lot of fun in Ishigaki. You can kayak the ocean or the mangroves. Though you`ll have to join a tour. The main places to kayak are Fukido river, Miyahara river, or Maezato beach (you can rent a kayak here).
Here are so companies you can look into if you`re looking for a kayak tour.
Ishigaki is a pretty big island so if you want to check out all the sites, you`ll definately need to rent a car! There are many car rental places and the prices are pretty reasonable, you can rent a car for as low as 4000 yen per day! So depending on where your hotel is, it`s a good thing to consider.
Go Diving / Snorkeling
Dive in the beautiful ocean and swim with the fish and look at the beautiful corals!