Sheikh Omar Abdel Rahman, a blind cleric who preached at mosques in NY, was sentenced to life in 1996 for planning the attacks.
A United States representative is learned to have made a phone call to his son Ammar conveying the death news.
The Egyptian radical Sheikh Omar Abdel-Rahman died at about 5:40 a.m. of natural causes battling long with diabetes and coronary artery disease at the Butner Federal Medical Center in North Carolina.
"America will go and be withered and this civilization will be destroyed", Abdel-Rahman said in Manhattan Federal Court.
It failed to do this but still killed six people and injured more than 1,000.
The blind Egyptian cleric was the spiritual leader of Al-Gama Al-Islamiyya.
According to Reuters, U.S. officials claimed that a computer error was responsible for Abdel-Rahman being given a visa.
He was accused of issuing a fatwa which led to the assassination of Egyptian President Anwar Sadat in 1986, but was eventually acquitted. American authorities blamed a computer error for the visa, but the mistake in 1991 when Abdel-Rahman was given a green card and permanent USA resident status.
Rahman was serving a life sentence on terrorism-related charges.
Abdel-Rahman would then travel to the U.S. in 1990 where he preached in Brooklyn, New York and New Jersey mosques, according to federal prosecutors.
The defendants were not directly charged with the 1993 World Trade Center attack but were convicted of conspiring with those who did carry out the bombing. Abdel-Rahman also preached his jihadi rhetoric at mosques in Jersey City, N.J., where he lived for a time.
Seven other defendants received prison terms of 25 to 35 years for planning what prosecutors called a "war of urban terrorism" aimed at altering US policy in the Middle East.
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