Like the rest of the network, they suffer from over-use and chronic under-investment.
Damage caused by Hurricane Sandy in 2012 has not yet been repaired.
Another storm, a tunnel crack or a high-speed derailment would be catastrophic.
Richard Barone of the Regional Plan Association, a think-tank, puts it bluntly: “We're operating on borrowed time.”
The NEC is, however, the only part of Amtrak that turns a profit.
Amtrak is an odd entity, a commercial service which has its board appointed by the president and receives funding from Congress.
Since the funding comes annually, Amtrak struggles to have a multi-year capital plan.
With a repairs backlog estimated at $28bn, and tunnels and track needing upgrades all over the region, it cannot do much beyond basic maintenance.
Congress is said to be increasing Amtrak funding to $1.5bn this year, $105m more than last year.
That is pretty small beer where railway tunnels under rivers are concerned.
The proposed Gateway tunnel, a new $24bn rail link between Newark, New Jersey and New York City under the Hudson river, would help to ease pressure on the network.
Last year the federal government agreed to split the cost with New York, New Jersey and Amtrak.
But little federal money has been spotted yet.
Meanwhile, the subway is still operating on a 1930s signal system; Eastside Access, a plan to bring some LIRR riders to Grand Central station, is delayed; the bus terminal needs a complete overhaul; the area's three major airports are at capacity.
But getting big projects built in New York is a costly, lengthy enterprise thanks, in part, to expensive labour and over-regulation.
The Second Avenue subway, the first new line in decades, cost $5.5bn for four miles of track and three new stations.