About 65 of the 243 people who were on the train were also injured, reports said.
An Amtrak power outage stalled their own trains and New Jersey Transit lines, officials said.
The LIRR and New Jersey Transit both reported disruptions after a wire fell in Penn Station.
Service changes will also affect Empire Service between New York City and Albany.
The rail agencies won't let straphangers bring alcohol onto its trains Saturday afternoon through Sunday.
NJ Transit trains were delayed up to an hour after signal problems temporarily suspended service.
Airports reported flight disruptions and NJ Transit announced that it will cross-honor tickets Friday.
The National Weather Service has issued coastal wind and flooding advisories.
Roadways like the Grand Central Parkway and Van Wyck Expressway could have up to 90-minute delays.
Large trucks were allowed back in the tunnels on Nov. 16, 2012.
Eight vehicles were involved in the noon smashup at the tunnel, officials said.
A collision between two buses forced some commuters to walk through the tunnel.
The M and 7 lines began providing modified service Friday morning, the MTA announced.
DNAinfo.com New York is tracking transit openings and closings after Hurricane Sandy.
Signal problems at New York Penn Station snarled trains to and from Manhattan.
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