I would go with a variation of the second alternative. Ideally, the identification of the locations should be of parallel construction. This is a problem carried over from the original in which initially the proper name of the mountain is positioned as a parenthetical remark, but the following proper name of the lake is placed as the direct object.

Located in this mountainous land are Pico Duarte, the Caribbean's highest mountain, and Lake Enriquillo, the region's largest lake and lowest elevation.

In the above sentence, if we strip out both parenthetical remarks, we still have a parallel sentence, that is basically: "Located here are Pico Duarte and Lake Enriquillo."

I kind of like the following alternative as well, moving the names to the subject position:

Pico Duarte, the Caribbean's highest mountain, and Lake Enriquillo, the Caribbean's largest lake and lowest elevation, are both located within this same mountainous area.

If we abandon "located," we have other, even more direct alternatives, including:

This mountainous region includes Pico Duarte, the Caribbean's highest mountain, and also Lake Enriquillo, the Caribbean's largest lake and lowest elevation.