"The MTA is an authority where the governor has a majority of appointees. So, ultimately, accountability lies on the governor," Pataki said on "Squawk Box."
Pataki spoke a day after a subway train derailed in Upper Manhattan, injuring 34 people and halting service on four busy lines. The MTA apologized on Twitter for the "service disruption" the derailment caused and later blamed it on human error, not a track defect, according to The Associated Press.
Service was restored Wednesday morning, though riders were told to expect residual delays. Cuomo called the derailment "an unacceptable manifestation of the system's current state."
The derailment came as New York subway passengers have witnessed delays, power outages and mechanical failures at some of the city's busiest stations.
In April, a New Jersey Transit train derailment took out several tracks at New York's Penn Station, creating long delays. That derailment came a week and a half after an Amtrak Acela train derailed there, causing disruptions for thousands of commuters.
Last month, Cuomo told CNBC that Penn Station is "crumbling by the day," and has requested for aid.
CNBC has reached out to governor's office for comment.
— The Associated Press contributed to this report.