They were stopped early Tuesday morning on the New Jersey side of the tunnel, which leads into New York City.
During a subsequent search of the vehicle, officers found rifles, loaded handguns and ammunition. The men are in their 50s and the woman is in her 20s and all three are white, NBC New York reports.
Almost 100,000 cars pass through the tunnel connecting the two states each day.
Police originally stopped the auto for having a cracked windshield. The three people were arrested. Police also found a camouflage helmet and what appeared to be night goggles.
The arrest of the trio, believed to be residents of Pennsylvania, was smooth and there was no stand-off with police, officials noted.
Three people in the van were taken into custody.
The suspects were still being interviewed by police Tuesday afternoon and it is not clear what charges they could face.
The FBI’s field office in New York City and the Port Authority of New York and New Jersey have not yet responded to RT’s request for comment.
At least one of the men arrested in the Brooklyn ISIL cell had expressed “interest” in shooting Federal Bureau of Investigation agents and police officers for the terrorist group.
Port Authority police didn’t immediately respond to a message from NJ Advance Media seeking additional information.