Per Amtrak's Website:
"Amtrak will provide modified Northeast Regional service between Newark, N.J., and points south, on Wednesday, October 31, including restoring Virginia service to Lynchburg, Richmond and Newport News. Amtrak will also operate Keystone Service trains between Harrisburg, Penn., and Philadelphia, and modified Downeaster servicetrains between Boston and Portland, Maine, along with some overnight services to and from the Northeast.
However, as in the case of other tunnel owners and operators in New York City, Amtrak is removing water and making repairs to track, signal and power systems within its tunnels under the Hudson and East rivers. The amount of water intrusion into the tunnels is unprecedented – as was the storm itself – so a date for restoration of Amtrak service directly to/from New York Penn Station from either the north or south is not available at this time.
Therefore, there will be no Northeast Regional service between Newark and Boston and no Acela Express service for the length of the Northeast Corridor on Wednesday, October 31. Also, at Newark Penn Station, there will be no connecting service to New York City and no elevator or escalator service. Service to the Newark Liberty Airport rail station is suspended due to a lack of connecting services.
Also canceled on Wednesday, October 31, is the Empire Service between New York City and Buffalo/Niagara Falls, the Adirondack to and from Montreal, Québec, Canada, and the Ethan Allen Express to and from Rutland, Vt., due to track damage south of Albany-Rensselaer, N.Y.
Other service plans, full and partial service, for Wednesday, October 31:
Crescent (Trains 19 & 20) will operate only between Washington D.C. and New Orleans
Cardinal (Train 51) will operate only between Indianapolis and Chicago
Auto Train (Train 52) will operate as schedule as scheduled between Sanford, Fla., and Lorton, Va.
Maple Leaf (Trains 63 & 64) will operate only between Toronto, Ontario, Canada, and Albany-Rensselaer
Carolinian (Trains 79 & 80) will operate only between Philadelphia and Charlotte
Silver Star (Trains 91 & 92) will only operate between Miami and Jacksonville, Fla.
Silver Meteor (Trains 97 & 98) will operate between Washington D.C. and Miami
Lake Shore Limited (Trains 448 & 449) will operate normally between Chicago and Boston, with no (Trains 48 & 49) service to points south of Albany-Rensselaer.
The following trains are also canceled for Wednesday, October 31:
Shuttle trains, Springfield, Mass.-New Haven, Conn.
Capitol Limited (Trains 29 & 30), Chicago-Washington, D.C.
Pennsylvanian (Trains 42 & 43), Pittsburgh-New York City
Auto Train (Train 53), Lorton, Va.-Sanford, Fla.
Vermonter (Trains 55 & 56), St. Albans, Vt.-Washington, D.C.
Palmetto (Trains 89 & 90), New York-Savannah
Customers are encouraged to monitor Amtrak.com/alerts and those Northeast Corridor passengers on Acela Express, Northeast Regional or Keystone Service trains can follow @AmtrakNEC on Twitter to be notified when updates are posted on Amtrak.com. Amtrak will also be providing updates on its Facebook.com/Amtrak and Twitter.com/Amtrak pages.
Amtrak will update this statement by Wednesday evening, October 31.
Passengers who have paid but choose not to travel due to this service disruption can receive a refund or a voucher for future travel. Some tickets booked online that have not yet been printed can be modified or canceled on Amtrak.com or by using the free Amtrak mobile app.
To be notified of major service disruptions resulting in delays of 60 minutes or more to multiple trains on the Northeast Corridor, follow @AmtrakNEC on Twitter.
Amtrak regrets any inconvenience. This information is correct as of the above time and date. Information is subject to change as conditions warrant. Passengers are encouraged to call 800-USA-RAIL or visit Amtrak.com/alerts for Service Alerts and Passenger Notices. Schedule information and train status updates are available at the Amtrak.com home page."
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So, to summarize--the tunnels are flooded into NYC. That is why they're not open, and given the scale of the flooding and overall damage, expect things to take quite awhile to get back online. This is a historic system. Based on this, its not going to be "days", its going to be weeks to months. Meanwhile, NJ Transit reports their headquarters is (verbatim) "underwater", and incredibly damaged. It would also seem (and this is just my positing however I digress), that this would likely end up resulting in a delay in the eventual upgrade of the corridor for higher speeds. Resources will need to be devoted simply towards restoring service, including the disaster for New York Penn Station etc... rather than upgrading the line from 135 to 160 or 150 to 160, depending on whether we're talking about NJ or MA/RI.
~SSD