The location of the third chart differs between the two versions:

On Wii U, Triforce Chart 3 is located on A-5: Needle Rock Isle and leads to G-6: Cliff Plateau Isles. Engage the ships near the isle in battle and destroy the golden gunboat to retrieve the chart.

On GameCube, Triforce Chart 3 is located on G-5: Bird's Peak Rock and leads to C-5: Stone Watcher Island.