Hynes was appointed the 24th New York City Fire Commissioner by Mayor Edward I. Koch on November 5, 1980 upon the resignation of Augustus A. Beekman.

In 1985, Governor Mario Cuomo appointed District Attorney Hynes as Special State Prosecutor for the New York City Criminal Justice System.

The race had attracted considerable attention because Mr. Hynes, a fixture in Brooklyn politics, was seen as vulnerable after four terms in office.

As a result, O'Hara, who admits that he had voted in his girlfriend's district, was disbarred, paid a $20,000 fine, and served 1,500 hours of community service.

In 2009, the state Supreme Court's Appellate Division unanimously approved a report by a state judicial committee that found that O'Hara's prosecution was unjustified; the report said, "Mr. O'Hara, accurately it appears, claims that [Hynes' political] machine went gunning for him and pounced on his change of residency calling it election fraud."

[14][15] In 2001, civil court judge John Phillips announced his intent to oppose Hynes in that year's race for district attorney.

Shortly afterward, Hynes' office began an investigation that resulted in claims that Phillips was the victim of a real estate scheme, and that the 70-year-old judge was incompetent to handle his own affairs.

[19][20] Between 2003 and 2007, Hynes prosecuted former assemblyman and Kings County Democratic Party chief Clarence Norman Jr., four times on four separate political corruption indictments.

[21] Hynes has also successfully prosecuted two former Brooklyn Supreme Court Justices, Victor Barron and Gerald Garson, for taking bribes.

[22][23] In 1998, after being kidnapped, blindfolded, bloodied, and stun-gunned by hooded assailants of the New York divorce coercion gang over the issuance of a get (religious divorce document), Abraham Rubin took his case to the New York City Police Department, but it was dropped by Hynes' office because the victim could not identify any of his assailants.>[24] Newsday interviewed an additional dozen residents in the neighborhoods of Borough Park and Midwood, Brooklyn, all of whom claimed that they were harassed, threatened, or assaulted by men working for their estranged wives.

[26] Hynes was also criticized for alleged reluctance in prosecuting cases of sexual abuse against children in ultra-Orthodox communities, which make up a significant segment of Brooklyn.

"[27] The editorial focused in particular on the case of Rabbi Yehuda Kolko, a Brooklyn yeshiva teacher charged with sexually molesting several students.

In a plea bargain, Hynes allowed Kolko to plead guilty only to two misdemeanor counts of child endangerment; he was sentenced to three years' probation.

[28] Following the Kolko case, Hynes' office started a program in 2009 called Kol Tzedek (Hebrew for Voice of Justice) to focus on and provide support for ultra-Orthodox sexual abuse victims.

[29][30] In January 2013, shortly before the sentencing of Satmar Hasidic counselor Nechemya Weberman for repeatedly abusing a young girl, Hynes published an editorial in the Daily News in which he wrote, "I hope the verdict and sentence sends a very clear and unmistakable message to people in certain parts of the Orthodox community — it is time to start protecting victims rather than defendants.

Collins had been sentenced to 34 years to life in prison, but won the right to retrial after the district attorney's office admitted that a key witness had recanted his testimony in the presence of a prosecutor before trial, and that this information had not been disclosed to the defense.

In a hearing for the lawsuit, Judge Frederic Block said Vecchione's behavior in Collins' trial had been "horrendous" and asked the lawyer for the city, "Hynes hasn't treated it seriously, has he?

",[42] Hynes sent the Voice a lengthy rebuttal which called their story "highly biased journalism" and "totally one-sided."