With all three pearls in his possession, Link can place them on the triangle islands.
Southern Fairy Island
Your next destinations are the Triangle Islands, which are marked on the map, but before you go, you can get an upgrade to carry more bombs.
First, go northeast. You'll probably encounter enemies on the way, so have your boomerang or bombs ready. Also, remember to avoid the giant cyclone if you see it. You'll pass Shark Island on the way.
Before going to the southernmost place marked on your sea chart, you can go to the island in the square directly south of it. It's Southern Fairy Island, where there are electrified Blue Chuchus (use your Boomerang to stun them), and where you can get an upgrade to carry more bombs. Just bomb the planks and go inside, then walk up to the fairy to get the upgrade.
The Triangle Islands
From the fairy island, go N to reach Southern Triangle Island. Just walk up to the statue here to place the pearl. Afterward, set the wind N and go two squares north. You'll pass Six-Eye Reef on the way.
After placing the pearl at Northern Triangle Island, you can go east to the fairy island. Use a bomb to get the big rock out of the way, then go inside to get another bomb upgrade. Now you can hold 99.
Then just go southeast. You might have a treasure chart for Eastern Triangle Island. The treasure here contains 200 rupees.
Finally, place the pearl at Eastern Triangle Island and watch the cutscene. Then you can optionally find the fish guy somewhere around the tower and get this square marked on the sea chart. Otherwise, press R to cruise, or change the wind direction and set sail, to enter the Tower of the Gods.