Police accused Zazi of receiving explosives training from al-Qaeda and plotting to undertake the attack with homemade bombs.
Alleged Pakistan visit
Zarein Ahmedzav, a 24-year-old of Afghan origin, was also arrested on Friday while working as a taxi driver and charged on the same day with making false statements to the Federal Bureau of Investigation (FBI) to which he pleaded not guilty.
In particular, Ahmedzav is accused of lying about where he had visited Afghanistan and Pakistan.
Medunjanin and Ahmedzav attended high-school with Zazi, 24, and investigators allege that the trio travelled to Pakistan together to attend an al-Qaeda training camp in 2008.
The three men are all from the New York district of Queens.
Robert Gottlieb, the lawyer for US citizen Medunjanin, said: "We entered an emphatic not guilty."
Gottlieb did not comment on the nature of his client's relationship with the other men or the circumstances of his arrest.
But he did accuse the police of holding Medunjanin for two days without access to a lawyer or his family, calling the questioning "illegal".
Gottlieb said he would seek to make any statements made during that time inadmissible.
Viktor Pohorelsky, the district judge, scheduled a detention hearing for Medunjanin for January 14.
Medunjanin and Ahmedzav had their homes raided in September after being linked to the bomb plot and had been under surveillance since Zazi's arrest.
Police said that they had gone to Medunjanin's apartment on Friday, with the intention of only seizing his passport, but that he fled in his car prompting a chase and his eventual arrest.
Gottlieb said that the car incident had been exaggerated, adding: "Let's see what the evidence is."