The Gateway project is considered critical to the greater metropolitan New York City area, which produces 10 percent of the country's economic output, according to the U.S. Census Bureau.
Contractors may also have to bore through a historic century-old granite bulkhead along the river shoreline, the documents show. Reuters also reviewed public records and conducted interviews with transportation officials and industry sources.
Construction would not begin until at least 2019, according to public records.
"The disruptions could be horrible," the transportation sector source told Reuters.
Manhattan's far West Side also is grappling with disruptions from the massive 28-acre Hudson Yards mixed-use real estate development project that straddles the existing rail connections.
Amtrak's current century-old tunnel, a few blocks north of where the new one would enter Manhattan at 29th Street, was damaged by flooding during 2012's Superstorm Sandy, which left behind a corrosive residue. It would undergo repair and renovation once the new tunnel is operational.
The new tunnel could cost between $5 billion and $7 billion, a transportation industry executive familiar with the project told Reuters on the condition of anonymity because the figures are early non-public estimates.
The federal government agreed to pay for half the project, with the two states splitting the rest, though it was unclear where New York and New Jersey will get the money.
A Port Authority of New York and New Jersey commissioner said on Thursday that $2.7 billion for the project could be included in the agency's next capital budget.
The Gateway project's advance comes just as President-elect Donald Trump assumes office. During his campaign he pledged to spur $1 trillion of infrastructure investment.
During environmental reviews for big public works, engineering firms often seek to identify the worst-case construction scenarios, industry sources said.
"We are going through this process to see what is the best way to construct the tunnel with the least amount of impact to everyone involved," said Nancy Snyder, spokeswoman for NJ Transit, which is leading the environmental review.
"No construction methods are finalized," she said, calling Reuters' information "incomplete."
The impact on New Jersey will likely be minimal, sources told Reuters, because the concepts contain a footprint already approved as part of a similar project called Access to the Region's Core (ARC), which New Jersey Governor Chris Christie canceled in 2010. Christie said at the time that the $12.4 billion project was too expensive.
Of two main ideas taking shape, the more intrusive one calls for contractors to dig up a partially renovated section of New York's Hudson River Park under a "cut and cover" concept. This would limit public access and lead to lane closures on the West Side Highway, a major thoroughfare.
Contractors will likely also need to stabilize the ground for tunnel boring using so-called freezing methods that involve permanently hardening the ground because parts of Manhattan sit on landfill.
"That turns it into a tundra, and it solidifies over time," said Denise Richardson, executive director of The General Contractors Association of New York Inc, one of several experts who reviewed the documents at Reuters' request.
Contractors will also likely build an underwater concrete encasement for the tunnel to come up through the New York side of the river.
The encasement, itself larger than a football field, would counteract buoyancy and protect the tunnel from anchors, grounded ships and other risks. It is expected to remain hidden below the waterline. Work in the water could span two years and encompass 224,000 square feet.
Affected onshore areas would be restored after the completion of the project, the documents showed.
Martin Robins, a former ARC project director who also reviewed the documents, said the potential construction impact on the surrounding area might be limited.
"I don't believe that it will have a dramatic effect," he said.