First, go to the Ocean Realm. Drive across the Train Tracks that are placed above the Ocean~Water. If you haven't noticed already, Jellyfish will appear sometimes while crossing over there. They came back from Phantom Hourglass.
If you haven't played Phantom Hourglass, this method is similar to the one in that game.
As soon as you see the Jellyfish, stop the train. Make sure you have the Jellyfish in sight, and no Pirate Ships are going to attack you. Use the cannon to hit the Jellyfish repeatedly. Each time you hit the Jellyfish, you get a Rupee. Make sure that the Jellyfish won't go into the water, because it will disappear if it does. Eventually, the Jellyfish will split into two.
Now, you can get Rupees 2x faster. The same thing continues on, you hit the Jellyfish with your Cannonballs and they will eventually split into two again.
However, the Jellyfish tend to separate and go into different directions quickly when splitting apart. It makes it harder to hit both of them quickly enough so they won't sink into the ocean.