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WEEHAWKEN, N.J. — The dirtiest work happened while most of New Jersey slept, on boats docked across from Manhattan’s shimmering, half-lit skyscrapers.

Employees of New York Waterway, a tour boat operator and the country’s largest private ferry company, would uncap a silver pipe and attach a small pump, forcing unfiltered waste from the boats’ toilets directly into the Hudson River, two former workers claim in court documents unsealed on Friday.

The practice went on for years, according to the former employees, who have filed a whistle-blower complaint in federal court in Newark accusing New York Waterway of violating the federal Clean Water Act.

“Anything that goes into a toilet would come right out,” said Rafi Khatchikian, 42, who was responsible for fueling and cleaning ferries at the company’s work dock in Weehawken. He worked the graveyard shift from September 2013 to August 2015, when he was fired after a diesel spill.

“It’s, like, blended when it comes out,” he said. “It looks like oatmeal.”

Once, after a large tour boat outing, Mr. Khatchikian said the pump spewed waste into the river for more than 45 minutes.

The company denies the allegations.

“We think it’s totally without merit,” said Armand Pohan, the company’s chairman.

Mr. Khatchikian and a second employee, Ivan Torres, said they were acting on instructions from their bosses at New York Waterway, a company that before the pandemic shuttled more than 30,000 passengers a day across the Hudson, a service it marketed as “the civilized commute.”

Mr. Torres said the practice was part of the reason he walked off the job in 2015 and moved with his wife and two children to Florida, where he does maintenance work near Orlando.

“It was horrible,” said Mr. Torres, a mechanic who said he began working for New York Waterway in 2011. “You’d go home and go to sleep and your nostrils still smelled of it.”

New York Waterway was founded in 1986 by Arthur E. Imperatore Sr., a onetime trucking magnate who died last month at 95.

A spokesman for the company, Patrick Smith, said the lawsuit was filed by “disgruntled ex-employees.” He cited the decision by a federal prosecutor not to bring charges in the case as evidence the claims were “baseless.”

A spokesman for Craig Carpenito, the United States attorney in New Jersey, had no immediate comment.

“After years of investigation, the U.S. Attorney’s Office has declined to participate in this meritless lawsuit, which was filed by two disgruntled ex-employees of NY Waterway,” Mr. Smith said in a statement. “The government’s decision in that regard speaks volumes about the baseless nature of these claims.”

Michael Baldassare, a criminal defense lawyer hired by New York Waterway to address the lawsuit, declined to comment.

Under federal law, whistle-blowers who disclose environmental fraud are eligible to be paid as much as 30 percent of fines recouped from polluters.

The allegations had been under investigation by the Environmental Protection Agency’s criminal investigation division for more than two years, according to records obtained by The New York Times through the Freedom of Information Act.

Are you a current or former employee of New York Waterway, the Environmental Protection Agency or the Coast Guard with a story to share? Contact us by sending us a confidential tip. We offer several ways to get in touch with and provide materials to our journalists.

The E.P.A. inquiry began in July 2016 and appeared linked not just to the claims raised by the two men. Another employee, a captain, had expressed similar concerns, according to the records, which were heavily redacted.

The captain, who the records suggest had been suspended after a boating accident, told the E.P.A. that “mechanics would plug in a pump right into the sewage and pump the sewage into the water (Hudson River),” a September 2016 investigation report states.

The captain’s goal, reports show, was to return to work to “get video evidence of illegal sewage dumping.”

Mr. Torres said he had done just that two years earlier.

In a nighttime video with an Oct. 6, 2014, time stamp shared with The Times, a man can be heard stating that he is pumping waste into the river as the camera shows what appears to be liquid flowing from a hose. “It’s done on a regular basis,” the man says in the recording.

Jeff Tittel, director of the New Jersey Sierra Club, a nonprofit environmental watchdog, said the E.P.A.’s failure to pursue criminal penalties had caused untold harm to a river slowly recovering after decades of contamination.

A segment of the 315-mile river was once a federal Superfund site, teeming with toxic PCBs, a synthetic chemical. But a dredging effort that began in 2009 has helped turn the Hudson into a watersport playground safe for kayakers, paddle boarders and the occasional wayward seal.

On Oct. 4, 2018, Mr. Khatchikian’s lawyer, Michael D. Fitzgerald, notified New York Waterway that a complaint would be filed and asked the company to preserve all evidence.

Twenty days later, E.P.A. agents boarded three ferries to try to place “concentrated green dye” in toilets to track the path of the wastewater, records show.

The toilet on one ferry had been removed altogether. The bathrooms on two other ferries were locked from the outside.

E.P.A. investigators had interviewed a New York Waterway vice president months earlier, who, records show, told them that “the boats do not have the ability to discharge directly into the water anymore.”

The vice president, whose name was redacted, said that “if it happens, it is not company procedure.”

A spokeswoman for the E.P.A., Mary Mears, said the agency had closed the investigation in December 2018, but reserved the right to “investigate any significant new information.”

“E.P.A. took the allegations very seriously and we launched an in-depth investigation,” Ms. Mears said in an email.

She said the agency “did not find the evidence that it would have needed to request that the U.S. attorney bring formal charges.”

Mr. Khatchikian said that on the nights he worked, he was the only employee responsible for emptying the ferries’ waste tanks and refueling boats.

He said he believed he was instructed to use a small, hand-held pump to discharge waste into the river because of a shortage of employees and the difficulty of proper disposal.

A long hose that was needed to hook boats to the lone stationary pump on the dock that could dispose of sewage properly froze in cold weather, he said. The legitimate pump also lacked the power to push the waste as far, or as fast, as it needed to go, he said.

“It took longer to do it the right way,” Mr. Khatchikian said in an interview. “The illegal pump pumps very quickly — much, much faster.”

Mr. Khatchikian was fired after a fuel spill. His termination letter claimed he left a fuel nozzle unattended and was “observed being inattentive.”

Mr. Torres, 36, said he spoke to two E.P.A. investigators who came to his house in Florida, but declined to give them the video and photos he had taken out of fear of self-incrimination.

“I’m going to make a very powerful man very angry,” he said about the company’s owner, “and what am I going to have to show for it?”

He added, “You think they’re going to make a movie about me because I ratted out the New York Waterway?”

Mr. Torres was recently added to Mr. Khatchikian’s lawsuit, providing him whistle-blower status and the promise of being eligible to share in a percentage of any potential fines generated by the lawsuit.

A federal prosecutor who works for Mr. Carpenito, the U.S. attorney in New Jersey, participated in the E.P.A. investigation, records show. But on Friday, Mr. Carpenito filed paperwork signaling that he had no plan to intervene in the case.

It has been clear for years that the financial stakes are high.

As part of the inquiry, Mr. Fitzgerald hired a private investigator, Bari Kroll, and rented an eighth-floor apartment on the Weehawken waterfront for five months in 2018 to conduct round-the-clock video surveillance of New York Waterway’s work dock.

On Oct. 3, 2018, at 4:20 a.m., Ms. Kroll said her surveillance cameras captured a greenish orb in the water near a ferry named the Bayonne, less than a day after E.P.A. records show that an agent had placed green dye in the toilet.

Mr. Fitzgerald shared the video with the E.P.A.

An E.P.A. report from the next day acknowledged that a ferry crew member appeared to spot something unusual in the river, leading the worker to shine a flashlight toward the water.

“When the flashlight shines on the water,” the report states, “there are brief moments when the water appears to have a greenish tint.”

The allegations involve a time when New York Waterway was preparing to vacate, or overhaul, its Weehawken work dock.

With one foot out the door, the company would have had little incentive to upgrade its balky sewage disposal system and could explain why it required employees to take environmentally damaging short cuts, Mr. Fitzgerald said.

In 2017, New York Waterway spent about $11.5 million to purchase waterfront land in neighboring Hoboken, N.J., where it hoped to build a new work dock. It had been trying to buy the parcel for 10 years.

The purchase, which impeded Hoboken’s plans to connect its waterfront amenities, became the subject of intense rancor and political intrigue. The dispute is unresolved.

There have since been signs of wear and tear on New York Waterway’s fleet.

Last year, the Coast Guard briefly pulled 23 of the company’s 32 boats out of service after deeming them “operationally unfit.”

“I just don’t think that they wanted to put up the money to set up the pumping that they had to, to do this the right way,” Mr. Fitzgerald said.

Derek M. Norman contributed reporting.

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