As Gov. Andrew M. Cuomo runs for a third term, the subway is a thorn in his side.

Mr. Cuomo is expected to easily win re-election Nov. 6. But that doesn’t mean New Yorkers are happy about his management of the crumbling transit system.

A new ad by Marcus J. Molinaro, his Republican challenger, features Twitter posts from angry subway riders and declares: “Under Andrew Cuomo the #MTA is derailing,” referring to the Metropolitan Transportation Authority, which runs the subway .

Mr. Molinaro has offered his own transit agenda, which focuses on reducing construction costs.

Mr. Cuomo, a Democrat, helped create the subway crisis by failing to adequately support the system — his administration even diverted transit funding to ski resorts — and he has been pilloried by subway advocates for prioritizing aesthetics over maintenance.

But the governor, who declared the subway to be in a state of emergency last year, has also won praise for hiring Andy Byford, a highly respected transit executive who introduced a $40 billion overhaul plan to save the subway. Mr. Cuomo supported the agency's roughly $800 million subway repair plan and has committed about $8 billion from the state for capital spending. And Mr. Cuomo revived a push for congestion pricing, a proposal to raise money for public transit by tolling vehicles entering Manhattan’s busiest areas, even though it carries political risks.