Gov. Andrew Cuomo on Thursday declared the MTA to be in a "state of emergency." Thomson Reuters

Gov. Andrew Cuomo declared on Thursday that the Metropolitan Transportation Authority was in a "state of emergency," as issues continue to plague the New Jersey Transit, Long Island Rail Road, and New York City subway systems.

The declaration comes after yet another morning of commuting woes. On Thursday, a power issue left hundreds of LIRR commuters stranded outside Penn Station for two hours, NBC New York reported.

Cuomo is giving his newly appointed MTA chairman, Joseph Lhota, 60 days to assess capital needs for cars, tracks, and signals. Cuomo also said he would add $1 billion to the MTA capital plan.

Cuomo ultimately controls the funding of the state-operated MTA. He is responsible for appointing six out of 14 MTA board members, giving him a plurality of votes.

Amtrak is set to begin long-overdue rail repairs at Penn Station in just a few weeks. Both the LIRR and the NJ Transit run on tracks along the Northeast Corridor, which Amtrak owns. Heavy delays along the lines are expected once work begins.

Cuomo has taken heat from New York City commuters who feel he has neglected existing transit options while setting aside funding for massive infrastructure projects, like a train connecting LaGuardia Airport to the subway and the LIRR.

Several issues have plagued the MTA of late: