ProPublica, co-recipient of the public-service award, was never publicly ridiculed by Trump, although White House press secretary Sean Spicer did refer to the outlet as a "left-wing blog" at a recent press briefing.
Over 35 days in the Philippines, Daniel Berehulak captured the images of 57 people killed in a brutal campaign that President Rodrigo Duterte has called a crackdown on drugs.
The Pulitzer Prize is the fifth awarded to a publication in the Bay Area News Group.
Mr David Fahrenthold of The Washington Post on Monday won the national reporting award for what the Pulitzer board called "a model for transparent journalism" that cast doubt on Mr Trump's assertions of charitable generosity.
Reporter Eric Eyre of Charleston Gazette-Mail in West Virginia took the prize for investigative reporting for exposing a flood of opioids in depressed West Virginia counties with the country's highest overdose death rates.
To celebrate 100 years of the Pulitzer prize, and the achievements of all the winners, the Philadelphia Inquirer, Philadelphia Daily News and philly.com joined with the Pennsylvania Humanities Council to mark the anniversary year with a special look at winners in all categories.
The New York Daily News and ProPublica garnered the coveted Pulitzer Prize for public service for uncovering abuse of eviction rules by police that drove many poor minority families from their homes.
The prize for explanatory reporting went to the International Consortium of Investigative Journalists, McClatchy, and the Miami Herald, for the Panama Papers stories on offshore tax havens. The Mercury News staff won the general news reporting prize the same year for its coverage of the natural disaster.
Also nominated as finalists: The Atlanta Journal-Constitution staff for a series revealing the prevalence of sexual misconduct by doctors; and Renee Dudley, Steve Stecklow, Alexandra Harney and other members of the Reuters staff for uncovering a US college admissions process corrupted by systematic cheating on standardized tests in Asia.
Lynn Nottage won the drama award for "Sweat", a play which was described as "a nuanced yet powerful drama that reminds audiences of the stacked deck still facing workers searching for the American dream".
"The Chicago Tribune" on the Pulitzer Prize for feature photography for portraying a 10-year-old boy and his mother striving to put the boy's life back together after he survived a shooting in Chicago.
The Pulitzers are awarded at Columbia University and handed out in 14 categories of reporting, photography, criticism and commentary by newspapers, magazines and websites. Public service award winners receive a gold medal; the other awards carry a prize of 15,000 US dollars each. A board of editors, publishers, writers and educators voted on 21 categories of journalism, letters, drama, poetry and music.