They’re operating in the green!

The highest-paid doctors in New York City are raking in millions of dollars each year, with some, even at struggling hospitals, getting six-figure bonuses, a Post review of hospital-based MDs has found.

The city’s top earner was urologist and prostate-cancer specialist Dr. David ­Samadi, whose 2012 compensation came to $7.6 million. He was chief of robotics and minimally invasive surgery at Mount Sinai Hospital before moving to Lenox Hill Hospital last June.

Not far behind Samadi was his Mount Sinai colleague Dr. Andrew Hecht, head of spine surgery, whose compensation came to $6.9 million.

Both doctors were paid by Mount Sinai’s Icahn School of Medicine.

“Whenever I see compensation data in health care, I’m stunned and nauseated,” said Dr. John Santa, medical director of Consumer Reports Health. “I’m embarrassed for the profession.”

Even the president of Mount Sinai Hospital, speaking at a conference last year, noted the “obscene levels” of pay for the hospital’s interventional cardiologists, specialists who clear blocked arteries, according to a report in Bloomberg News.

The hospital’s head of interventional cardiology, Dr. Samin Sharma, made $4.8 million in 2012.

Mount Sinai’s interventional-cardiology program, the busiest in the country, is under scrutiny after a Bloomberg report last month found that some heart patients were coming in for scheduled procedures through the emergency room. The practice raised questions about whether this was a way to have the “emergency” treatment covered by insurance.

Like many hospitals, Mount Sinai pays doctors based on a formula that includes how many and what type of procedures they perform.

“Mount Sinai’s compensation packages are important recruitment and retention tools in an exceedingly competitive health-care-delivery environment. They also relate to productivity and performance,” a hospital spokesman said.

Seventy-five percent of doctors were offered a salary plus a bonus when hired in 2012-13, according to a report by Merritt Hawkins, a physician- ­recruitment firm.

In New York, those ­bonuses can sometimes reach Wall Street levels.

Columbia University Medical Center dermatology professor David Silvers got a $2.2 million bonus in 2011 on top of his $3 million salary, according to the university’s most recent tax filings.

Silvers runs the laboratory that does skin biopsies.

“Compensation is based on a combination of factors, including research and clinical work as well as teaching and administrative responsibilities,” said medical-center spokesman Douglas Levy.

Spine surgeon Anthony Frempong-Boadu’s bonus at NYU Langone Medical Center came out to $3.2 million in 2011, according to the tax filing for New York University.

An NYU spokeswoman said the money was not a bonus but rather the surgeon’s compensation based on his productivity.

Bronx-Lebanon Hospital, which operated at a $4 million deficit in 2012, still found the cash to pay ­bonuses to its top docs.

Dr. Magdy Mikhail, head of obstetrics and gynecology, was paid a salary of $283,427 and a bonus of $999,500. Dr. John Coffey, the chairman of emergency medicine, took in $520,795 in salary plus an $800,000 bonus.

“If the bonus is just based on just bringing more income in, that’s not very comforting,” said Arthur Levin, the director of the Center for Medical Consumers, an advocacy group.

A Bronx-Lebanon spokesman said he would not discuss the employment terms of any hospital doctors.