The passenger, identified as Khalil El Dahr, had to be restrained to a chair with several seatbelt extenders for the rest of the flight.
According to the affidavit, Mr Dahr had reportedly attempted to make a phone call mid-air but was livid after he was unsuccessful. Less than 30 minutes in the air, he reportedly got out of his seat and rushed towards the cockpit screaming in Spanish and Arabic, asking to be shot.
He was initially "corralled" by an attendant before a crew officer opened the cockpit door. Mr Dahr punched and kicked a flight attendant on his chest before strangling him with the crew's tie while trying to move towards the cockpit.
The passenger "grabbed the JetBlue attendant by their collar and tie with one hand while using his other hand to grab the overhead compartment to gain leverage to kick," the affidavit said.
After kicking the crew member the passenger allegedly again asked to be shot.
During the assault it took six to seven crew members to restrain the passenger with plastic zip-tie handcuffs, the Daily Beast reported.
The man however managed to break out of them and later was strapped to a seat using four seat belt extenders at the rear of the plane.
Law enforcement officials met the crew upon its arrival in San Juan.
Meanwhile, the US Justice Department and officials in six states filed a lawsuit to block a partnership between JetBlue and American Airlines over claims that it will lead to higher flight fares. The companies announced their deal last year and have started coordinating flights in the Northeast.