Millions of people were without power on Wednesday after fallen trees downed power lines.
The sound of generators and chainsaws punctuated the sunrise in New Jersey, where more than one million homes and businesses were without electricity.
NJ Transit train service remained suspended while crews cleared about 150 trees and repaired signals and overhead wires.
Regional rail services were also suspended in Philadelphia after Isaias raised the Schuylkill River and sent an unsecured construction barge into a bridge.
Inspectors were checking for damage. Interstate 676, which crosses the bridge, was also closed in both directions.
Patrick Foye, chairman of New York’s Metropolitan Transportation Authority, said more than 2,000 trees fell across the system’s train and bus network.
“This storm caused severe damage,” Mr Foye said on Wednesday. “Not since Superstorm Sandy has our system experienced this type of wind.”
Two people died when Isaias spun off a tornado that struck a North Carolina mobile home park.
Another person died in Pennsylvania when their vehicle was overtaken by water and swept downstream.
The five-year-old girl had gone missing from her Philadelphia-area home during the height of the storm Tuesday and was found dead on Wednesday. Authorities said they believed she was swept away by floodwaters in the creek behind her house.
Three others were killed by falling trees toppled by the storm in Maryland, Connecticut and New York City, and another person died in Delaware when a tree branch fell on them, authorities said.
A woman was found dead inside a New Hampshire house on Tuesday evening.
Isaias sustained top winds of up to 65mph more than 18 hours after coming ashore, but it was down to 40mph maximum winds as of early Wednesday, according to the National Hurricane Centre.
Before making landfall late on Monday, Isaias killed two people in the Caribbean and battered the Bahamas before brushing past Florida.
Tornadoes were confirmed by the National Weather Service in Virginia, Maryland, Delaware and New Jersey.
Power outages also spread as trees fell, with more than 2.7 million customers losing electricity across multiple states as of Wednesday morning, according to PowerOutage.US, which tracks utility reports.
New York City’s power utility said it saw more outages from Isaias than from any storm except Superstorm Sandy in 2012.