Web sites www.NJTransit.com and www.MNRR.com, www.LIRR.com and www.MTA.com all have bits of information. Basically, SEPTA operations went back at noon Tuesday, but the NYC area is in bad shape. NJT reports the bridges hit on the NJCL and washouts on the NJCL and Atlantic City lines; trees across the tracks and wires down (catenary presumably) all over; power to the computer system that "operates the railroad" along with back up power, etc. have all been flooded making things difficult to ascertain. Other than the specifics on the Coast and Atlantic City lines and the loss of the operations computers, very they are revealing very little...including the snake bit Port Jervis line and the Pascack Valley line they operate for MNRR. MNRR is showing pictures on its site of the flooding at Harmon and elsewhere on the Hudson LIne, several locations on the Harlem Line and the New Cannan branch, as well as pics of the LIRR's Oyster Bay branch tree across the track, some washouts, and the flooding of West Side Yard...just west of NYP...in Manhattan. Subways and PATH all suffering from salt water covering the track and third rail power and needs to be "cleaned" before even thinking of running power through much less a train. MNRR did run a diesel powered inspection train on the Harlem but I got that from posted pictures on Facebook.
As an aside...as far as the computer being flooded and all power and back up power non existant. Few people knew this, but the DL&W RR had a back up dispatchers office at Denville, NJ station with two desks and complete phone and telegraph connections so that if anything ever happened in Hoboken, the were still able to operate everything from Denville. It was a double desk, back to back, so that the dispatchers would have faced each other and was located in the ticket office to the M&E track side. Telephones, earphones, telegraph keys, and the code dialers were all there! EL pulled it out, maybe CR. But the point is that there was a back up operations plan and location to execute that plan. Sure its sexy to have the Empire State, Wall St., and the Statue of Liberty in view and the mass complex of tracks and equipment spread out for all to see. And those cute Transit Villages around the track or tracks look nice and should bring in some money while the sale or demolition of old stations help the till, too. But it seems that a hideaway in the hills with a full communications set up, a back up in case of a total loss of the main frame of operations, would seem like an appropriate investment. In NJT's defense, I would say that I never heard that Denville was ever used under any circumstances. But right now, it would seem that a Denville like back up would certainly make tomorrow look easier to achieve.