The three - Dhiren Barot, Nadeem Tarohammed and Qaisar Shaffi - are being held in Britain on charges that they plotted attacks with radioactive or chemical weapons and are not expected to stand trial until later this year.
US authorities said they would seek their extradition after their trials. White House press secretary Scott McClellan said President George Bush was pleased by the indictments.
All three face life in prison if convicted. They have been charged with conspiring to use a weapon of mass destruction, conspiring to aid terrorists, aiding terrorists and conspiring to damage or destroy commercial buildings.
The alleged plot to bomb the World Bank and International Monetary Fund headquarters in Washington, the New York Stock Exchange and Citigroup headquarters in Manhattan, and the offices of Prudential Financial in Newark was first revealed on 1 August, when US authorities issued a heightened alert and increased security around the buildings.
The three suspects were among eight people detained in Britain on 3 August, after Pakistani authorities captured a massive al-Qaida database containing information on possible targets, reportedly including surveillance data on the US buildings.
The US indictment says Barot, Tarmohammed and Shaffi plotted together from 1998 until their arrest, and visited and conducted video surveillance on their potential targets between August 2000 and April 2001.
According to the indictment, Barot, also known as Isa al-Hindi, "served as a lead instructor at a jihad training camp in Afghanistan where recruits were taught to use weapons and received other paramilitary training".
In 2000 he travelled to the US where he applied to college in New York, and, while he was admitted, never enrolled in any classes, authorities said.
Washington accuses him of using the college admission to "conceal the true purpose of his subsequent trips to the United States" from Britain.