The US believes the jet was shot down by the Soviet Union, claiming the life of an American diplomat.
There are long-standing rumours that the Soviets later raised the plane in secret. The incident took place just before the Soviets invaded Estonia.
The six-day operation in the Baltic by a US Navy oceanographic survey ship ended on Wednesday morning.
Estonia asked the US to help solve the mystery over the fate of the plane. The aircraft was carrying nine passengers and crew. None survived.