The Pacific island used to portray 'Dante' s Island' in the episode is the Japanese island of Iwo Jima, the location of the famous WWII battle of the same name. In the image of the island, shown when Malcolm is first describing it's location (about 11mins 18secs into the episode), Mount Suribachi can be clearly seen in the foreground. Mt. Suribachi is the location of the famous flag raising by US Marines immortalized in the iconic photo taken by Joe Rosenthal on February 23, 1945.
The villain's super secret, super secluded, and super private island deep in the Pacific (2,688 Kilometres from the nearest point of land) far from everywhere, as shown on the screen at 11:17, is actually Iwo Jima with the distinctive Mount Suribachi on the southern tip.