The Pulitzer for breaking news was awarded to The Boston Globe for its coverage of the deadly Boston Marathon bombing.
The awards are American journalism's highest honor.
The winning entries about the NSA's spy programs showed the government has collected information about millions of Americans' phone calls and emails based on its classified interpretations of laws passed after the Sept. 11 attacks.
The disclosures touched off a furious debate in the U.S. over privacy versus security and led President Barack Obama to impose limits on the surveillance.
The New York Times won two Pulitzers in photography: Tyler Hicks was honored in the breaking news category for documenting the Westgate mall terrorist attack in Kenya, and Josh Haner was cited for his essay on a Boston Marathon bomb blast victim who lost his legs.
The Center for Public Integrity won the award for investigative reporting for reports on how some lawyers and doctors rigged a system to deny benefits to coal miners suffering from black lung disease.
The Pulitzer for explanatory reporting was given to The Washington Post for reporting on the prevalence of food stamps in America.
No award was handed out for feature writing.
The winners of the public service award receive gold medals. The other awards carry a $10,000 prize.