Investigators had already found the sunken ship and debris on the ocean floor, but had not found the recorder, which they believe holds clues to the the final hours of the El Faro.
"Finding an object about the size of a basketball almost three miles under the surface of the sea is a remarkable achievement," Christopher A. Hart, chairman of the NTSB, said in a statement Tuesday. The agency posted video of the recorder on YouTube.
The NTSB had said earlier this month that it would resume the search for the missing data recorder, which the agency says could hold "critical information" for investigators. While the device was found at about 1 a.m. early Tuesday morning, authorities now say the next step is to figure out how they can actually retrieve it.
This device could contain navigational data as well as voice recordings from the navigation bridge of the ship in the hours before it went down during Hurricane Joaquin.
El Faro was heading from Jacksonville, Florida, to Puerto Rico in October when the ship sent out electronic distress alerts amid a report of some flooding. The NTSB said in a preliminary report that the Coast Guard and the ship's operator were unable to reestablish communication after that. In the days that followed, authorities found a debris field and damaged rafts, but the Coast Guard soon declared the ship lost and suspended the search for any survivors. There were 28 Americans and five Polish workers killed in the incident.
Before the ship sank, one of the crew members wrote in an email that El Faro was encountering difficult seas and heavy winds due to the hurricane.
"Not sure if you've been following the weather at all, but there is a hurricane out here and we are heading straight into it," Danielle Randolph wrote to her mother, Laurie Bobillot.
When the sunken ship's wreckage was found last fall, video footage found that the navigation bridge and the deck below had separated from the ship itself. The sinking of the El Faro brought renewed attention to the dangers involved in cargo shipping.
A research vessel owned by the U.S. Navy will remain in the area near the sunken ship to document it through Saturday before returning to Massachusetts, the NTSB said.
