The findings were recently published by the Tree-Ring Society.
Molly McDonald remembers the moment they found the ship. She was on the scene with AKRF - an environmental, planning, and engineering consulting firm - which had been hired to monitor the excavation project.
Until then, the team had uncovered buried wharves and piers that once formed the city's shoreline, but were later filled and built on.
But that day - July 13, 2010 - they diggers noticed something different. Backhoes had raked across curved timber in the outline of a ship, McDonald said. They stopped the machinery and started digging gently. Immediately, McDonald said, she knew the discovery was big.
"You don't think it's actually going to happen," she said.
McDonald said she stood there, with the noise of New York City around her, and pictured being at the bottom of the Hudson River - "a surreal juxtaposition," she said.
Then a lengthy process began: excavating, dismantling, recording, and documenting so the ship might be reassembled. Individual lengths of timber were 3-D laser-scanned, tagged, wrapped, and finally loaded on a truck headed for the Maryland Archaeological Conservation Laboratory.
Samples of timber were sent to Columbia University's tree-ring lab at the Lamont-Doherty Earth Observatory, where researchers worked to determine how old the wood was and where it came from, a process called dendrochronology.
Much of the wood is from white oaks, which are found across the Northern Hemisphere, said Dario Martin-Benito, lead researcher of the study.
But then the team caught a break. It found that the ship's keel was made of hickory, found only in the eastern United States and eastern Asia, he said. Now, the team knew where to concentrate.
The next step was to compare samples of the boat's wood to "master chronologies," or wood from the same area that has already been dated. Martin-Benito likened the process to comparing bar codes.
The team compared the samples to 21 oak chronologies from the eastern United States, and the World Trade Center ship most closely matched two: one from Philadelphia, the other from eastern Pennsylvania.
The signs pointing toward Philadelphia did not stop there.
Because of "idiosyncrasies" in the construction of the ship, and the lack of variation in the timber, archaeologists determined that the ship had likely been built at a small, rural shipyard, McDonald said. Such a shipyard would be more likely to get all of its timber from the same area.
This solidified the Philadelphia theory. During the colonial era, Philadelphia had an extensive shipbuilding industry. McDonald said that archaeologists surmised, based on the tree-ring data, that the ship was likely built at a small shipyard on the outskirts of Philadelphia.
When nautical archaeologist Warren Riess got to the site, he first thought the vessel was a brigantine, but after the ship was excavated and the archaeologists got a better look, they thought they had found a large Hudson River sloop.
Those sloops were made for river travel and transported cargo and people, Riess said. Though the boat was made near Philadelphia, Riess said it was likely meant to sail in the trade areas around New York, Connecticut, and the Chesapeake.
But the wood had been infested by shipworms that are found only in warm salt water, which seems to indicate that it had traveled at least once to the Caribbean, Martin-Benito said.
Hudson River sloops were "made by the hundreds," Riess said, though very little is known about them. Few have been recovered. Such boats remained in use even after steamboats were invented, he said, citing paintings into the 1800s, in which both sloops and steamboats are depicted.
"It didn't take the world's best shipwrights to make it, but it might've been some very good shipwrights," he said. Despite its craftsmanship, the boat was not in use long. The ship was built shortly after 1773, and the area where the ship was found was filled in by the 1790s. McDonald said the worm infestation might have led to its abandonment.
Sometimes, McDonald said, ships are sunk to become part of a landfill on purpose. But that did not happen to this ship. The oysters growing on the ship indicated it had been at the bottom of the river for a while, maybe a year or two, before the area was filled, she said.
With the ship, archaeologists found cannonballs, a spoon, ceramics, buckles, pipe fragments, a button with the insignia of the British 52d Regiment, and a coin stuck to the bottom of the hull - so deteriorated, McDonald said, that it could not be read.
Though it was McDonald's first time working on a ship, she had heard that this was a common, superstitious practice.
But Riess is doubtful. Though he had often read about the practice when he started researching board, he said, he had never found an example of it.
"And we've looked," he said, with a laugh.
Riess can't say for sure - maybe the coin was put there on purpose and the myth has come to life - but if he had to guess, Riess said, he thought someone probably just dropped it.
Martin-Benito said he did not think there was much left to discover in New York. But after working on the World Trade Center ship, he realized he was wrong.
"There's still some mystery down there," he said.