The PATCO Speedline between southern New Jersey and Philadelphia was not operating during Wednesday's rush because of power problems. Trains were expected to be running after midmorning. New Jersey Transit has suspended service on its Atlantic City rail line.
The Southeastern Pennsylvania Transportation Authority suspended service along some regional rail lines.
Four people sustained minor injuries when a building collapsed in the Fishtown section of Philadelphia.
In New Jersey, nearly 200,000 homes and businesses were without electricity Wednesday morning after the storms, some packing 75 mph winds, thundered through the region.
Gloucester, Camden and Salem counties were among the hardest hit areas. Complete utility restoration could take several days.
The NWS is investigating whether a tornado formed in parts of Gloucester County.
Strong winds ripped off part of the Deptford Mall's exterior. More than 30 animals were left stranded when a pet shop roof fell in in Gibbstown.
Parents and students scrambled when the storms formed as the Egg Harbor Township High School graduation ended.
There are no reports of injuries.
In New Hampshire, the fast-moving storm knocked out power in Colebrook, Columbia, Pittsburg and Stewartstown, but most service was restored before morning.
The strong storm system was the same that had spawned tornadoes in the Midwest, including at least nine in northern Illinois.
As the storms moved through southeastern Pennsylvania on Tuesday evening, the sky blackened and commuter train service was halted beginning at rush hour. Amtrak suspended its Northeast Corridor and Keystone services from Washington through Philadelphia and on to Harrisburg, Pennsylvania, but restored service about two hours later.