Police dived in after the teenager, but were unable to save him.
The car, which a woman's body was rescued from last Wednesday, appears to have gone over the falls Saturday night amid heavy winds and rising water in a storm.
Police said the unidentified woman in her late 60s who died in the car appears to have driven into the river on purpose, and the investigation is ongoing.
A rescuer, equipped with an ax, a yellow helmet, goggles and a snorkel, swayed to and fro in the wind as they tried to reach the submerged car.
Despite evidence to the contrary, some fans viewed the video as proof a second season is on the way..
The woman, named Tianna Natasha McPherson, is facing accusations of assaulting, resisting or impeding a U.S. officer.
Zhao Yan was mistaken for a drug smuggler and received bruises to her face during her arrest at the U.S.-Canada border in 2004.
Kirk Jones was the first person to survive the drop from the falls without a safety harness in 2003.
"If a guy can do it, a girl can do it too," said Nik Wallenda's wife, who broke her husband's world record.