President Obama said in a written statement that Thomas "never failed to keep presidents – myself included – on their toes."
"What made Helen the 'Dean of the White House Press Corps' was not just the length of her tenure, but her fierce belief that our democracy works best when we ask tough questions and hold our leaders to account," said Obama, the last president in a string dating back to the 1960s to field questions from Thomas.
Thomas was known to legions of Washington reporters simply as "Helen." She was the doyenne -- and, unofficially, the dean -- of the White House press corps since the Kennedy administration, but never succumbed to the allure of power, prestige and glitz surrounding the capital.
"There is something about the White House that seems to encourage secrecy," Thomas once said. "Our role is really to try to make presidents accountable. The media, is the only institution in our society that has the privilege of questioning a president on a regular basis and making him accountable."
Politico said word of Thomas' death was spread in an email from the Gridiron Club, a venerable association for Washington journalists.
"Former Gridiron Club president Helen Thomas, our first female member, died Saturday morning at her Washington apartment after a long illness," Gridiron's Carl Leubsdorf wrote. "She would have been 93 next month."
Thomas -- who frequently reminded colleagues that, "You're only as good as your last story" -- wrote three memoirs: "Dateline: White House" in 1975 , "Front Row at the White House" in 1999 and "Thanks for the Memories, Mr. President: Wit and Wisdom from the Front Row at the White House," in 2002.
"It is a sheer joy to know that the work you have dedicated your life to has impacted others," Thomas said. "It was never my intention to become a great personality, only a great reporter. Pleasure in your profession puts perfection in your work. It's a labor of love."
Former President Bill Clinton said in a statement Thomas "was a pioneering journalist who, while adding more than her share of cracks to the glass ceiling, never failed to bring intensity and tenacity to her White House beat."
"Throughout her career she covered the issues and events that shaped the course of our world with perseverance and a tough-minded dedication," Clinton said.
He praised Thomas' "commitment to the role of a strong press."
The White House Correspondents Association honored her in 1998 with its lifetime achievement award.
Clinton at the time called Thomas "a symbol of everything American journalism can and should be -- the embodiment of fearless integrity, fierce commitment to accuracy, the insistence of holding government accountable. All of that in the spirit of the First Amendment and the free press it protects."
Thomas was born Aug. 4, 1920, in Kentucky. She was one of six children of Lebanese immigrants and was raised in Detroit. She moved to Washington to take an entry-level job with the Washington Daily News. She joined United Press during World War II and joined UPI's White House bureau after John F. Kennedy was inaugurated in 1961.
She was the UPI White House bureau chief from 1974 until she left the wire service in 2000. She spent another 10 years as a columnist for Hearst Newspapers.
National Public Radio correspondent David Folkenflik said Thomas "broke barriers that prevented women from rising in the Washington press corps."
She was the first female president of the White House Correspondents Association and enjoyed the longest tenure of any member of the elite White House press corps.
Thomas' long career was not without controversy. She was known for asking blunt questions from her front-row seat in the White House press room and refusing to accept answers that were vague or off the subject.
CNN quoted Thomas saying, "I have never covered the president in any way other than that he is ultimately responsible."
Although she was well beyond retirement age, Thomas saw her career come to a premature end in 2010.
She became the target of outrage and controversy when she told an amateur videographer outside the White House that Israel should "get the hell out of Palestine."
Thomas later apologized for the remarks but did not back down from her opinion.
"They do not reflect my heartfelt belief that peace will come to the Middle East only when all parties recognize the need for mutual respect and tolerance," she said in a subsequent column. "May that day come soon."
Although Thomas was known for being prickly and not easily intimidated, she was also highly respectful of her position and always maintained she "felt very privileged to cover the White House."
"I see people peering through the gates and know they would love to be inside and know what's going on," Thomas said. "I wish the doors could be as open to them as they have been to me."
Her family said Thomas will be buried in Detroit, where she grew up, CNN reported. A memorial service is planned in Washington in October, her family said.
Thomas, a graduate of Wayne State University, married Douglas Cornell, who died in 1982.