Earlier, police said the death was caused by a possible drug overdose and appeared to be accidental.
Ledger was known for grueling, intense roles that became his trademark after he got his start in teen movies like "10 Things I Hate About You."
The Australian-born actor was found dead Tuesday abround 3:30 p.m. by his housekeeper and masseuse - lying naked and face-down at the foot of his bed, with prescription sleeping pills nearby, police said. They tried to revive him, but he was already dead.
His death was shocking, an unforeseen end to one of Hollywood's brightest young stars. Ledger was 28 years old.
The Australian-born actor came to Hollywood in the late 1990s determined to shake his pretty-boy image.
"He took on the most challenging, the most serious, the most demanding roles and delivered every time," said Jeanne Wolf, West Coast Editor of "Parade" magazine.
Ledger was found face down and naked on his bed.
"There were some prescribed medications that included sleeping pills found in the apartment," said NYPD Spokesman Paul Browne.
Authorities say there was no obvious indication that Ledger had committed suicide.
Outside the building on an upscale street, hundreds of photographers and onlookers craned their necks as officers brought out a black body bag on a gurney.
Ledger was an award-winning actor who chose his roles carefully, rather than cashing in on big-money parts. He was nominated for an Oscar for his performance in "Brokeback Mountain." That's where he met actress Michelle Williams, who played his wife in the film. The two have a 2-year-old daughter together.
Ledger's career will continue posthumously. He'll be seen on the big screen this Spring as the macabre Joker in the "Batman" sequel, "The Dark Knight."
In 2000, he starred opposite Mel Gibson in "The Patriot."
Tuesday, Gibson said in a statement: "I had such great hope for him. He was just taking off and to lose his life at such a young age is a tragic loss." Though his leading man looks propelled him to early stardom in films like "10 Things I Hate About You" and "A Knight's Tale," his career took a notable turn toward dramatic and brooding roles with 2001's "Monster's Ball."
Ledger's publicist, Mara Buxbaum, said in a statement: "We are all deeply saddened and shocked by this accident. This is an extremely difficult time for his loved ones and we are asking the media to please respect the family's privacy and avoid speculation until the facts are known."
In the Australian city of Perth, where Ledger was born and raised, his father called the actor's death "tragic, untimely and accidental."
"He was (a) down-to-earth, generous, kind-hearted, life-loving, unselfish individual, extremely inspirational to many," Kim Ledger said, reading from a prepared statement. "Heath has touched so many people on so many different levels during his short life."
Ledger eschewed Hollywood glitz in favor of a bohemian life in Brooklyn, where he became one of the borough's most famous residents. "Brokeback" would be his breakthrough role, establishing him as one of his generation's finest talents and an actor willing to take risks.
Ledger began to gravitate more toward independent fare, including Lasse Hallstrom's "Casanova" and Terry Gilliam's "The Brothers Grimm," both released in 2005. His 2006 film "Candy" now seems destined to have an especially haunting quality: In a particularly realistic performance, Ledger played a poet wrestling with a heroin addiction along with his girlfriend, played by Abbie Cornish.
But Ledger's most recent choices were arguably the boldest yet: He costarred in "I'm Not There," in which he played one of the many incarnations of Bob Dylan - as did Cate Blanchett, whose performance in that film earned an Oscar nomination Tuesday for best supporting actress.
And in what may be his final finished performance, Ledger proved that he wouldn't be intimidated by taking on a character as iconic as Jack Nicholson's Joker. Ledger's version of the "Batman" villain, glimpsed in early teaser trailers, made it clear that his Joker would be more depraved and dark.
Ledger told The New York Times in a November interview that he "stressed out a little too much" during the Dylan film and had trouble sleeping while portraying the Joker, whom he called a "psychopathic, mass-murdering, schizophrenic clown with zero empathy."
"Last week I probably slept an average of two hours a night," Ledger told the newspaper. "I couldn't stop thinking. My body was exhausted, and my mind was still going." He said he took two Ambien pills, which worked for only an hour, the paper said.
Ledger was a widely recognized figure in his Manhattan neighborhood, where he used to shop at a home and children's store. Michelle Vella, an employee there, said she had frequently seen Ledger with his daughter - carrying the toddler on his shoulders, or having ice cream with her.
"It's so sad. They were really close," Vella said. "He's a very down-to-earth guy and an amazing father."
Before settling down with Williams, Ledger had relationships with actresses Heather Graham and Naomi Watts. He met Watts while working on "The Lords of Dogtown," a fictionalized version of a cult classic skateboarding documentary, in 2004.
Ledger was born in 1979 to a mining engineer and a French teacher and got his first acting role playing Peter Pan at age 10 in a local theater company. He began acting in independent films as a 16-year-old in Sydney and played a cyclist hoping to land a spot on an Olympic team in a 1996 television show, "Seat."
After several independent films, Ledger moved to Los Angeles at age 19 and starred opposite Julia Stiles in "10 Things I Hate About You." Offers for other teen flicks soon came his way, but Ledger turned them down, preferring to remain idle than sign on for projects he didn't like.
"It wasn't a hard decision for me," Ledger told the Associated Press in 2001. "It was hard for everyone else around me to understand. Agents were like, `You're crazy,' my parents were like, 'Come on, you have to eat."'
The Associated Press contributed to this report.