Luis Armando Pena Soltren entered the plea Thursday to charges of conspiracy to commit air piracy, interfering with a flight crew, and kidnapping.
The 67-year-old returned to the United States from Cuba last fall to face the federal charges.
Authorities said he and co-defendants brought pistols and large knives aboard in a baby's diaper bag. The pilots were forced to divert Puerto-Rico bound Pan American Flight 281 from Kennedy Airport to Havana.
The November 1968 flight had 103 passengers and crew aboard.