The Pulitzer for breaking news was awarded to The Boston Globe for its "exhaustive and empathetic" coverage of the Boston Marathon bombing and the manhunt that followed.
The winning entries about the NSA's spy programs revealed that the government has collected information about millions of Americans' phone calls and emails to try to head off another 9-11-style terrorist attack.
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.
Two of the nation's most distinguished newspapers, The Post and The New York Times, won two Pulitzers each.
The Pulitzer for explanatory reporting went to the Post's Eli Saslow for reporting on food stamps in America.
The New York Times won twice in photography: Tyler Hicks was honoured 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 blast victim who lost his legs.
The NSA stories were written by Barton Gellman at The Washington Post and Glenn Greenwald, Laura Poitras and Ewan MacAskill, whose work was published by The Guardian US, the British newspaper's American operation, based in New York.
"I think this is amazing news," Poitras said in New York. "It's a testament to Snowden's courage, a vindication of his courage and his desire to let the public know what the government is doing."
Snowden, a former contract employee at the NSA, has been charged with espionage and other offences in the U.S. and could get 30 years in prison if convicted. He has received asylum in Russia.
While his critics have branded him a traitor, others have celebrated the release of the documents, likening them to the Pentagon Papers, the secret Vietnam War history whose publication by The New York Times in 1971 won the newspaper a Pulitzer.
In a statement issued by the Freedom of the Press Foundation, Snowden called the award vindication for "everyone who believes that the public has a role in government."
He saluted "the brave reporters and their colleagues who kept working in the face of extraordinary intimidation, including the forced destruction of journalistic materials, the inappropriate use of terrorism laws, and so many other means of pressure to get them to stop."
At The Boston Globe, the newsroom was closed off to outsiders, and staff members marked the announcement of the breaking-news award — coming just a day before the anniversary of the bombing — with a moment of silence for the victims.
The attack last April 15 killed three people and wounded more than 260 near the finish line of one of the world's most celebrated races, transforming a celebratory event into a scene of horror and heroics.
American journalism's highest honour, the Pulitzers are given out each year by Columbia University on the recommendation of a board of distinguished journalists and others.
The two winners of the public service award will receive gold medals. The other awards carry a $10,000 prize.
The Center for Public Integrity's Chris Hamby won the award for investigative reporting for detailing how lawyers and doctors rigged a system to deny benefits to coal miners suffering from black lung disease.
The prize for national reporting went to David Philipps of The Gazette of Colorado Springs, Colorado, for an investigation that found that the Army has discharged escalating numbers of traumatized combat veterans who commit crimes at home.
The Pulitzer for international reporting was awarded to Jason Szep and Andrew R.C. Marshall of Reuters for their reports on the violent persecution of the Rohingya, a Muslim minority in Myanmar.
It was the news agency's first Pulitzer for text reporting.
The Oregonian newspaper was awarded a Pulitzer for editorial writing, with the judges honouring a selection of works that focused on reforms in the public employee pension fund. The prize was the third in the newspaper's history for editorial writing.
The Tampa Bay Times' Will Hobson and Michael LaForgia won in local reporting for writing about squalid housing for the city's homeless.
"These reporters faced long odds. They had to visit dicey neighbourhoods late at night. They had to encourage county officials to be courageous and come forth with records," said Neil Brown, Tampa Bay Times editor and vice-president. "And in the end, what they were ultimately doing was standing up for people who had no champion and no advocate."
The Philadelphia Inquirer's architecture critic Inga Saffron won for criticism. At The Charlotte Observer, Kevin Siers received the award for editorial cartooning for his "thought-provoking cartoons drawn with a sharp wit and bold artistic style."
No award was handed out for feature writing.
Sig Gissler, who administered the prizes at Columbia, said the reporters on the NSA story "helped stimulate the very important discussion about the balance between privacy and security and that discussion is still going on."
The Post's Gelman said the stories were the product of the "most exhilarating and frightening year of reporting."
"I'm especially proud of the category," he said. "Public service feels like a validation of our belief in the face of some pretty strong criticism that the people have a right to take part in drawing the boundaries of secret intelligence in a democracy."
Associated Press Writers Verena Dobnik and Deepti Hajela in New York, Steve LeBlanc in Boston, Eileen Sullivan in Washington, Tamara Lush in Tampa, Florida, and Nigel Duara in Portland, Oregon, contributed to this report.