LIRR trains were delayed 20 to 30 minutes and NJ Transit was delayed by up to an hour.
NJ Transit commuters faced delays of up to 30 minutes Wednesday morning.
An Amtrak power outage stalled their own trains and New Jersey Transit lines, officials said.
Normal service was restored to subway lines that experienced delays Monday morning.
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The rail agencies won't let straphangers bring alcohol onto its trains Saturday afternoon through Sunday.
LIRR administrators opted for the booze ban "based on experience," a spokesman said.
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Airports reported flight disruptions and NJ Transit announced that it will cross-honor tickets Friday.
Plans to improve the station include the installation of skylights, a new elevator and uniform signage.
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.
Signal problems at New York Penn Station snarled trains to and from Manhattan.
The company is reporting delays of up to an hour both in and out of Manhattan's Penn Station.
A disabled train caused delays of up to a half hour during the Tuesday evening rush.
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