Amtrak has completed its repairs to the problem, and the LIRR anticipates a normal rush hour Tuesday evening.
Commuters faced westbound delays averaging 75-90 minutes into Penn and some eastbound delays averaging 15 minutes. Some trains were canceled at Jamaica, or diverted to Hunterspoint Avenue or Atlantic Terminal.
The power issue occurred inside one of the East River tunnels, the MTA said in a statement. Amtrak personnel were working to correct the problem.
Two LIRR trains also were disabled in the East River tunnel, each stranded for more than an hour.
According to the MTA, one, which was carrying 1,000 passengers, was in the tunnel for 75 minutes.
A rescue engine was used to pull the disabled LIRR trains to Penn Station.
There were no injuries on the disabled trains, although the conductors distributed water.
NYC Transit was honored via the "E" subway between Jamaica and NY and via the "7" train between Woodside and New York as well as Hunters Point Avenue and New York.
Sources say Monday's incident is entirely unrelated to the ongoing track and signal problems beneath Penn Station.
Derailments and aging infrastructure have led to delays and disruptions for more than half a million daily riders on New Jersey Transit, Amtrak, and LIRR.