Here's an easy way to get as many rupees as you desire. While sailing the seas, you may from time to time encounter jellyfish-like creatures. When these are encountered, the ship should be stopped (though they will follow the ship even if you don't stop). Shoot these foes with the cannon (the cheapest cannon for your craft will only cost 50 rupees). When they are killed, they will drop a green rupee. Since they split apart when shot, you will be able to get multiple rupees per creature. Keep riding your ship around finding more of these creatures, and you can accumulate a good amount of rupees, as many as you'd like.