Prendergast has served more than three years as president of MTA New York City Transit, which runs the subway and bus system in New York City, and has served as the MTA Interim Executive Director since January 1, 2013.
He replaces Joseph Lhota, who resigned to pursue a Republican bid for New York City mayor.
"Tom Prendergast is a consummate public transit leader who is the ideal candidate to oversee the nation's largest transportation system," said Governor Cuomo.
"The MTA will improve the customer experience, operate more efficiently and build for the future. And we will aggressively rebuild smarter and better in the aftermath of Superstorm Sandy," Prendergast said.
The Governor's appointment of an MTA chairman and CEO is subject to Senate confirmation.
Prendergast is a career public transit officer and former MTA executive who was appointed President of MTA New York City Transit in November 2009. Prendergast, then the CEO at TransLink in Vancouver, B.C., returned to New York and took office December 1, 2009. He is a native of Chicago.
"Tom Prendergast has the hands on skill and long commitment to transit to make a great head of the M.T.A. The Straphangers' Campaign has found Tom to be accessible, knowledgeable, smart and fair," said Gene Russianoff, Staff Attorney for the NYPIRG Straphangers' Campaign.