Specialized machinery has been working to dig up the nearly 1,600 damaged concrete railroad ties to replace them with fresh ones.
Service was emporarily suspended for most of the day Sunday due to an early morning freight train derailment near New Haven, Connecticut.
Experts said the air was safe to breathe again Monday afternoon at the site of a train derailment in South Jersey.
Several tanker cars derailed in the accident around 7 a.m. on a rail bridge in Paulsboro and toppled into Mantua Creek.
The northbound 6 train derailed between Chambers and Centre street just north of the Brooklyn Bridge station around 3:52 a.m.
The incident — described as minor — happened around 6 p.m. Metro-North said there were no injuries.