David Malone was the third climber to attack the building's facade.
Malone, 29, said his July 9 ascent to the 11th floor was meant to publicize his book about terrorists, including Osama bin Laden and al-Qaida.
Malone's lawyer, Robert Gottlieb, says his client took "extraordinary" precautions to make sure nobody was hurt.
Gottlieb said after Malone's arraignment Thursday that the charges -- misdemeanor trespass and reckless endangerment -- are too serious for what he did.
Malone was ordered to return to court Nov. 18.