After unlocking Spirit Island and acquire the shovel, try this to get 1,000 rupees easily. First, head to the Spirit Island, where you can destroy all boulders. Then, defeat all of the enemies, and cut down all of the grass. Then, dig around. And finally, enter the cave, break all of the vases, leave the cave, and repeat the steps. Doing this will net you all of the rupees you want… if you're patient.