The best evidence of endosymbiotic theory is option 2: "Eukaryotic cells contain not only their own DNA, but some organelles contain their own unique DNA."
Endosymbiotic theory suggests that certain organelles, like mitochondria and chloroplasts, originated as free-living prokaryotic organisms that were engulfed by ancestral eukaryotic cells. The fact that these organelles have their own unique DNA, distinct from the nuclear DNA of the eukaryotic cell, supports this theory, as it indicates a shared evolutionary history. In contrast, the first option regarding chordates and their circulatory system does not provide specific evidence related to endosymbiosis.