He is following the path of his father, the late John Flanagan, who served in the New York State Assembly from 1972 to 1986. Senator Flanagan resides in East Northport with his wife, the former Lisa Perez of Maryland. Their two sons currently attend school in the Northport-East Northport School District while their daughter is attending college.Senator Flanagan currently serves as the Chairman of the Senate Standing Committee of Corporations, Authorities and Commissions and is a standing member of the Aging; Consumer Protection; Higher Education; Insurance; Labor; Tourism, Recreation and Sports Development; Transportation; and Veterans, Homeland Security and Military Affairs Standing Committees.He is a also member of the Task Force on Government Reform, the Task Force on World Trade Center Recovery, the Task Force on State and Local Emergency Preparedness and the Task Force on Children's Health and Safety.
In July of 2008, he was selected to serve on the powerful four-member Metropolitan Transportation Authority (MTA) Capital Program Review Board which is responsible for reviewing, monitoring and approving the MTA's multi-billion dollar five-year capital spending programs.