Police recovered a loaded Smith & Wesson .45-caliber handgun and a loaded Intratec Luger Tec-9 machine gun.
The NYPD says a police officer stopped the suspect after observing him Sunday evening entering the 42nd Street station in Manhattan without paying.
They say the officer then noticed the handgun in the man's waistband.
Police say the machine gun was found inside a bag the suspect was carrying.
Police identified the suspect as 33-year-old Allen Reggie of Columbia, S.C.
They charged him with criminal possession machine gun, criminal possession weapon loaded firearm and other charges.
It was not immediately known if he had a lawyer.
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