"There's nobody in this room who wanted to cover this story. Each and every one of us hopes that nothing like it ever happens again on our watch," Globe Editor Brian McGrory told the newsroom.
The bombing last April 15 that killed three people and wounded more than 260 also led to a Pulitzer in the feature photography category for Josh Haner of The New York Times, for his photo essay on a blast victim who lost his legs.
The Times also won in the breaking news photography category, for Tyler Hicks' coverage of the Westgate mall terrorist attack in Kenya.
The Washington Post and The Guardian won the Pulitzer Prize in public service for revealing the U.S. government's sweeping surveillance programs in a blockbuster series of stories based on secret documents supplied by National Security Agency leaker Edward Snowden.
The stories about the NSA's spy programs revealed that the government has systematically collected information about millions of Americans' phone calls and emails in its effort to head off terrorist attacks. The resulting furor led President Barack Obama to impose limits on the surveillance.
The reporting "helped stimulate the very important discussion about the balance between privacy and security, and that discussion is still going on," said Sig Gissler, administrator of the Pulitzer Prizes.
The NSA stories were written by Barton Gellman at The Post and Glenn Greenwald, Laura Poitras and Ewen MacAskill, whose work was published by The Guardian US, the British newspaper's American operation, based in New York.
Snowden, a former contract employee at the NSA, has been charged with espionage and other offenses in the U.S. and could get 30 years in prison if convicted. He has received asylum in Russia.
Snowden's supporters have likened his disclosures to the release of the Pentagon Papers, the secret Vietnam War history whose publication by The New York Times in 1971 won the newspaper a Pulitzer. His critics have branded him a criminal.
The Washington Post won a second Pulitzer in the explanatory reporting category, for Eli Saslow's look at food stamps in America.
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 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, Colo., 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 coverage of the violent persecution of a Muslim minority in Myanmar.
The Oregonian won for editorial writing for its focus on reforms in Oregon's 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 in Florida won in local reporting for writing about squalid housing for the homeless.
The Philadelphia Inquirer's architecture critic Inga Saffron won for criticism. At The Charlotte Observer, Kevin Siers received the award for editorial cartooning.
No award was handed out for feature writing.
In the arts categories, the fiction prize went to Donna Tartt for "The Goldfinch," while the general nonfiction prize was won by Dan Fagin, for "Toms River: A Story of Science and Salvation."
Alan Taylor won the history prize for "The Internal Enemy: Slavery and War in Virginia, 1772-1832" and the biography prize went to Megan Marshall for "Margaret Fuller: A New American Life."
The drama prize was awarded to Annie Baker for "The Flick" and Vijay Seshadri got the poetry prize for "3 Sections."
The music prize went to John Luther Adams for "Become Ocean."
Associated Press Writers Verena Dobnik and Meghan Barr in New York; Frank Eltman in Mineola, N.Y.; Steve LeBlanc in Boston; Eileen Sullivan in Washington; Tamara Lush in Tampa, Fla.; Nigel Duara in Portland, Ore.; Brett Zongker in Washington; and Kathy Matheson in Philadelphia contributed to this report.