It pays to work for the Port Authority — big time. The average salary at the bistate agency hit $90,000 last year — more than $30,000 above the average salary for private-sector workers in the city — according to a new analysis by the conservative think tank the Manhattan Institute.

The study found that average salaries at the PA rose about $1,000 over 2009, even as the agency is preparing to propose hiking bridge and tunnel tolls 25 percent next year, from $8 to $10.

“Is it bloat, or is it grounded in necessity? They need to show me,” said City Council Minority Leader James Oddo (R-Staten Island). “If they have a good explanation for it, they better put it out there rather quickly.”

According to the analysis, the highest-paid PA worker is executive director Christopher Ward, who earned $304,902. The agency’s top attorney, Darrell Buchbinder, was No. 2, with $251,758.

The most eye-popping numbers were put up by PA cops, four of whom made the top 10 thanks to huge overtime pay.

Three police sergeants more than doubled their base salaries because of OT. And one of them, Sgt. Edwin Rivera — No. 8 overall — pulled down $132,286 on top of his base salary of $103,964 to make him the PA’s OT champ for 2010.

Rivera declined to comment.

In a statement, the PA said it “has taken significant steps to control costs . . . the agency is now at its lowest staffing levels in 40 years and will continue its commitment to cutting costs.”

The agency has a workforce of about 7,000 — including a 1,500-member police department — and operates the region’s airports and seaports, the World Trade Center, the PATH train system, and the city’s Hudson River bridge and tunnel crossings.

By comparison, the Empire Center said the average employee salary at the MTA in 2009 was dramatically lower, at $69,000.

“We think it’s incredibly important that financial data, like the Port Authority’s payroll, is available for analysis,” the Empire Center said in a statement.

“It helps to paint the whole picture of where our tax dollars go and provides a canvas for taxpayers to make an informed decision about how they think their government is performing.”

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