Boyd had been diagnosed with lung cancer in February and died Thursday at his home, said his wife, Robin Stone. He had been sick for most of the year and had kept the condition private from most friends and colleagues, Stone said.
"Every wife would say she'd want her husband to be known as a great person, wonderful husband, father and good citizen," she said from her home. "But as I've said before, as a journalist, he was my hero; and I know he was a hero to many journalists in the profession."
Boyd and executive editor Howell Raines were brought down by the scandal caused by Jayson Blair, a journalist they had groomed, and criticism of their management style at one of the world's most distinguished newspapers. Boyd resigned in 2003.
Bill Keller, executive editor of the New York Times, called Boyd a friend and colleague. "He was one of us," Keller said in an e-mail to Times staff.
According to the newspaper's Web site, Boyd's career began during the civil rights era and inspired generations of black journalists.
He was the first black journalist to work the many jobs he held at The Times, including city editor. As deputy managing editor for news, he oversaw the 2000 series "How Race is Lived in America," which won a Pulitzer Prize.
At a lecture in St. Louis a few years ago, according to the Times' Web site, he told the audience, "Throughout my life I have enjoyed both the blessing and the burden of being the first black this and the first black that, and, like many minorities and women who succeed, I've often felt alone."
A native of St. Louis, he joined the Times in 1983 after serving as White House correspondent for the St. Louis Post-Dispatch. At 28, he was also the youngest journalist chosen for a prestigious Nieman fellowship at Harvard, The Times reported.
Since his resignation, Boyd wrote a weekly column for Universal Press Syndicate to help people understand how newsroom decisions are made.
"I just think the more we can as journalists try to explain what happens in terms of decision-making, to pull back curtains and describe what goes on in newsrooms or in journalism in general, the better we are," Boyd said in 2004.
Boyd joined Columbia University's Graduate School of Journalism for a semester in 2004 to develop case-study curriculum materials, and had been working on a memoir.
"I wanted to do everything I could to try to be a positive force in journalism and try to begin to deal with issues that I saw as important, such as credibility issues, such as leadership issues and issues involving diversity," he at the time.
In remarks made in the months after the Jayson Blair scandal, Boyd said he made a mutual decision with the newspaper to resign after The Times discovered that Blair had plagiarized material, invented quotes and wrote stories using datelines of places he had never been. The scandal exposed a deeply discontented staff that had lost confidence in newsroom leadership.
Boyd shared the blame and responsibility for Blair's downfall but said management didn't realize how deeply troubled Blair was until it was too late.
Had management known, "Jayson Blair simply would not have been writing for The New York Times," Boyd said at a speech made in Dallas in August 2003. He dismissed as "absolutely untrue" criticism that Blair had been promoted and his problems overlooked because the reporter was black.
Boyd said it was disturbing that people would read more into the situation because of race.
"I would be lying if I didn't say that I can't help wonder why after all these years of struggling to establish our work and credibility in the newsroom — to be seen as top-notch journalists — as soon as controversy arises, an African-American reporter and an African-American senior editor are automatically viewed as suspect," he said at the time.
He is survived by his wife and 10-year-old son Zachary.