All face charges of manslaughter, criminally negligent homicide and reckless endangerment.
"Everybody who could have screwed up, screwed up here," District Attorney Robert Morgenthau said of the fire.
The city had acknowledged failing to inspect the building for fire hazards but was not charged in the deaths, angering relatives of the dead firefighters.
While the city made major mistakes, governments are generally immune from criminal prosecutions under a centuries-old legal doctrine called "sovereign immunity," Morgenthau said.
Prosecutors did reach an agreement with the city and Bovis Lend Lease that requires them to institute major safety measures.
Mayor Michael Bloomberg said in a statement, "We will now be creating an additional civilian inspection unit at the Fire Department dedicated to construction, demolition and abatement sites."
The investigation concluded that breakdowns by the Fire Department and Department of Buildings "contributed to the conditions that led to the deaths" of the firefighters, prosecutors said.
Firefighters Robert Beddia and Joseph Graffagnino were found dead of smoke inhalation in the former bank tower, a building heavily damaged in the Sept. 11 attacks.
Galt was a subcontractor hired by Bovis and the building's owner, the Lower Manhattan Development Corp., to remove toxic debris from the building and take it down floor by floor. The 41-story tower had been dismantled to 26 stories before the fire. It remains at that height.