Heres 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 dont 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 youd like.

If you havent yet challenged Jolene to a final duel, go and find her. Battle her a couple of times. You will be rewarded with a large red rupee (worth 200 rupees) each time you do. This is especially useful for buying all of the 1,000 rupee items at Beedles and the Island Shops.