Ferid Imam was named in an indictment unsealed Tuesday in federal court in Brooklyn.
The new court papers allege Imam was part of a conspiracy to attack the subways with suicide bombers in September 2008.
Colorado airport driver Najibullah Zazi and another man have pleaded guilty to terrorism charges. A third man is awaiting trial.
News reports in Canada say Imam vanished from Winnipeg in 2007 and is suspected of hiding out in northwestern Pakistan.