The New York Times won three Pulitzer Prizes, and The New York Daily News and ProPublica shared the Pulitzer Prize for public service, as journalism presented its highest honors on Monday at a time of financial challenges for the industry and unabashed antagonism toward the news media from a new administration.

The Daily News-ProPublica won for a series on the New York Police Department’s widespread abuse of a decades-old law to force people from their homes and businesses over alleged illegal activity.

The investigation, which involved the examination of more than 1,100 nuisance abatement cases, found that the Police Department almost exclusively targeted households and shops in minority neighborhoods. The reporting drove New York City to re-examine the nuisance law and pass sweeping reforms.

The Times won three awards — for breaking news photography, feature writing and international reporting. Daniel Berehulak won for photographs that provided a haunting portrait of a violent campaign in the Philippines; C.J. Chivers won for a magazine piece on a young veteran of the war in Afghanistan suffering from PTSD; and reporters for The Times won for international reporting for a series on Russia’s surreptitious assertion of power.

Mr. Berehulak won in the feature photography category two years ago for his moving portraits depicting the spread of Ebola in West Africa.

David A. Fahrenthold of The Washington Post won the Pulitzer Prize for national reporting for his work on Mr. Trump’s charitable foundation.

Peggy Noonan of The Wall Street Journal won the prize for commentary for columns that the Pulitzer board said “connected readers to the shared virtues of Americans during one of the nation’s most divisive political campaigns.”

Colson Whitehead’s brutal and surreal novel “The Underground Railroad” won the prize for fiction, continuing Mr. Whitehead’s literary award sweep. The novel, which won the National Book Award last fall, centers on a young woman named Cora, who escapes her life as a slave on a cotton plantation in Georgia and flees via a real subterranean network of train cars.

Interactive Feature | The Times’s Pulitzer Announcement

The novel was a commercial and critical juggernaut — in The Times, Michiko Kakutani wrote that “Mr. Whitehead found an elastic voice that accommodates both brute realism and fablelike allegory, the plain-spoken and the poetic.” It was selected by Oprah Winfrey for her book club, and is being adapted into a limited drama series for Amazon by Barry Jenkins, the writer and director of the Academy Award-winning film “Moonlight.”

Mr. Whitehead, 47, said in a phone interview on Monday that to be given even more recognition by the Pulitzer committee was “startling and wonderful,” adding with a laugh, “Obviously, it’s all downhill from here.”

The drama critic Hilton Als of The New Yorker won for criticism, the second year in a row the magazine has won in that category. Last year, Emily Nussbaum won for her television coverage.

The Pulitzers this year come as newsrooms across the country face daunting challenges, with financial pressure draining many news organizations of the resources to pursue top-flight journalism. They also come in the face of a Trump administration that is openly hostile to much of the news media — Mr. Trump has called the news media “the enemy of the American people.”

But for one day, at least, newsrooms came together in celebration, and the journalism industry’s focus was on its accomplishments and purpose rather than its woes.

The International Consortium of Investigative Journalists, McClatchy and The Miami Herald shared the prize for explanatory reporting for their coverage of millions of leaked documents known as the Panama Papers. (The Miami Herald also won in another category — Jim Morin was awarded the prize for editorial cartooning.)

Eric Eyre of the Charleston Gazette-Mail won the investigative reporting prize for coverage that laid bare the relentless flow of opioids into West Virginia counties with the highest rate of overdose deaths in the country.

The East Bay Times of Oakland, Calif., won the breaking news reporting prize for its coverage of the “Ghost Ship” fire in December that killed 36 people at a warehouse party, chronicling the city’s failures that led to the tragedy.

The local reporting prize went to reporters at The Salt Lake Tribune for their reporting on the cruel treatment of sexual assault victims at Brigham Young University.