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Sharkey's 1994 book Bedlam: Greed, Profiteering, and Fraud in a Mental Health System Gone Craz is an investigation of the psychiatric industry. Focusing on sensational cases in the United States, Sharkey exposed how powerful elements within the industry maneuvered to exploit new markets when health insurance providers began covering costs for in-hospital mental health treatment. He traces soaring mental health costs to the often criminal marketing practices of biological psychiatry, which Sharkey asserts began when the number of psychiatric hospitals boomed in the late 1980s. He provides anecdotal tales of people coerced into treatment on fabricated pretenses, and compares schemes to fill beds at for-profit mental and addiction facilities, which were offering bounties to clergy, teachers, police and "crisis counselors," to the business plan of the Holiday Inn hotel chain.

The psychiatric industry, warned Sharkey (whose late father-in-law was a respected psychiatrist involved in setting up non-profit mental health clinics during the 1980s in New York state) has been lobbying legislatures for an increasing share of government health spending. Despite such warnings by Sharkey and mental health watchdogs, similar practices have continued to evolve in Texas (where many of the events depicted in Bedlam took place), in the form of the Texas Medication Algorithm Project, and at the federal level with the President's New Freedom Commission on Mental Health.

Another of Sharkey's books is Above Suspicion, the story of FBI agent Mark Putnam, who murdered his mistress in an eastern Kentucky mining town. In Suspicio, Sharkey implicitly condemns the FBI for encouraging the use of paid informants. "Above Suspicion" has been optioned by Reese Witherspoon's Type A Productions to be made into a feature film. His book Deadly Greed explores the sensational 1989 Boston killing, in which Charles Stuart fatally shot his pregnant wife Carol and caused racial tensions by accusing a black man of the crime.

Sharkey has also co-authored a novel, Lady Gold, with former New York Police Department detective Angela Amato. The movie rights for the book were purchased by Paramount Pictures and was in development by Mel Gibson's production company, Icon.

Joe Sharkey was one of seven people aboard an Embraer Legacy business jet involved in the crash of Gol Transportes Aéreos Flight 1907, using a Boeing 737-800, on September 29, 2006. The private jet lost a wing tip and part of its tail, but landed safely in a Brazilian military air base located in the Amazon jungle. The Embraer Legacy jet was owned and operated by ExcelAire Service Inc., a charter company headquartered in Ronkonkoma, New York. All 148 passengers and six crew members aboard the Gol Airlines Flight 1907 perished. The Legacy jet was on its maiden flight from Embraer's headquarters in São José dos Campos, near São Paulo, to the United States. Sharkey was on a freelance assignment in Brazil for Business Jet Traveler, a business magazine specializing in corporate aviation. Sharkey said the Legacy jet stabilized after the apparent collision, until it landed at the Serra do Cachimbo airbase in the state of Pará. In a New York Times front page article titled "Colliding With Death at 37,000 Feet, and Living", filed on October 1, 2006, Sharkey reported:

And it had been a nice ride. Minutes before we were hit, I had wandered up to the cockpit to chat with the pilots, who said the plane was flying beautifully. I saw the readout that showed our altitude: 37,000 feet. I returned to my seat. Minutes later came the strike (it sheared off part of the plane’s tail, too, we later learned).

During an interview with NBC's Today Show on October 5, 2006, Sharkey said he was relaxing in his cabin seat with the window shade down when he was jolted by a bang. "It was more like a car that hits a pothole rather than 'boom!'" he said. The plane steadied itself and it became serenely silent again. It was only when Sharkey opened the shade and looked out his window that he noticed something was dreadfully amiss. "My heart just sank because I looked at the wing tip and I saw that it was shorn off,” he told Today host Matt Lauer. "Basically four feet of the wingtip, the part that curves up, the winglet, gone... I’ve flown a lot, and I’m thinking, 'This is definitely, definitely not good.'"

The pilots, Joseph Lepore and Jan Paladino, were composed and focused, like "infantrymen who were well trained." Still, Sharkey and the other passengers, despite an uneasy calm, grew concerned. "It was very serene," Sharkey said. "At first it was just quiet and grimly concern." An engineer on board noticed the damaged wing was starting to peel, and Sharkey said it was then that everyone on board started to think about dying. "That’s the point in which it was clear that one way or another we were going down in unpleasant circumstances, and probably, since we couldn’t find a runway, we were going to ditch."

Sharkey scribbled a quick note to his wife, "I expressed my love, my appreciation and the fact that I accepted death." He put the note in his wallet, thinking it might eventually be found. "And then I thought it was almost bizarre Is this going to hurt? And how badly is it going to hurt?" The pilots eventually spotted a remote military airstrip and safely put the plane down. Sharkey said that when he found out, several hours later, that the Legacy jet hit a commercial airliner, he thought "We should not be the ones walking away from this." Asked, at the end of the interview, about the pilots who saved his life, he said: "I think we need to be careful about how the evidence is evaluated, because I think these guys are in some peril."

The NTSB released results of a preliminary analysis of the Legacy's flight data and cockpit voice recorder showing that the Legacy pilots had tried to contact air traffic control at least fifteen times in the thirty minutes prior the collision without success.

On his blog, “Joe Sharkey at Large” , Sharkey wrote about his experience and of being held for 36 hours for interrogation after the forced landing, his views on the ongoing investigation, and the public response against him and others aboard the Legacy jet. In response to Sharkey's questioning of Brazil's air traffic control infrastructure, Waldir Pires, the Brazilian Defense Minister stated:

"I cannot anticipate testimony that may be given, for example, by this [Joe Sharkey] in the United States. It is evident, it seems to me that his personality is a little frivolous, because with the number [of accidents] we have and the statements he makes, it [(Sharkey's statement)] is something absolutely inadequate."

Pires was later fired for his handling of aviation crisis of 2006-2007.