Prosecutors are allegedly looking into potential conflicts between Samson's private business interests and his unpaid role as the port's chairman.
Samson served as a New Jersey attorney general under then Gov. Jim McGreevey and also ran Christie's transition in 2009-2010.
The investigation by New York prosecutors comes as a result of an investigation by New Jersey federal prosecutors into a purported traffic study engineered as political payback in the state.
Traffic jams in Fort Lee and on the George Washington Bridge into New York City occurred from Sept. 9-13, and were believed to be aimed at Fort Lee Mayor Mark Sokolich. He did not endorse Christie for re-election.
Dozens of people have been subpoenaed in the New Jersey investigation, including people from Christie's inner circle, his re-election commission, and the state Republican Party.
The lane closings and traffic jams are being investigated by federal prosecutors in New Jersey. A source tells ABC News that the latest inquiry in New York will likely fold into the New Jersey investigation.
A spokeswoman for Samson issued the following statement Monday: "We are not commenting on the progress of investigations."
The Port Authority of New York and New Jersey runs the region's airports, Hudson River crossings and the World Trade Center.
ABC News and The Associated Press contributed to this report.