Perhaps in an effort to shut up critics who mocked its decision to close down systemwide, the MTA has photographs of flooded stations, tracks and railyards—even a mudslide at the Metro-North track near Spuyten Duyvil. NYCTSubwayScoop answered, via Twitter, the burning question of when would MTA service be back, "We have to assess the damage, dry out track, remove downed trees then get equipment back into place. No ETA."
The official MTA statement is, "There are already reports of flooding and down trees across the region, and the storm surge and heavy rains may cause additional widespread flooding, mudslides, washouts, fallen trees and downed power lines that wreak havoc on the MTA’s signals, tracks, stations, under-river tunnels, catenary wires and other infrastructure."
Back in 2007, an unusual tornado caused tons of flooding along the subway system, forcing the MTA to close the system during the morning commute.