The Cuomo administration’s inquiry into overpaid CEOs of nonprofits has taken its first scalp — one tellingly close to the governor himself.

Laurence Belinsky resigned last week, shortly after The Wall Street Journal reported that he’d been paid more than $500,000 in 2008 and 2009 as CEO and president of Help USA, a homeless-advocacy group.

HELP paid Belinsky $546,000 in 2008 — including a $157,000 bonus — and $508,000 in 2009, according to IRS filings.

Those filings also showed at least 10 other employees of the group — which has a $70 million annual budget — getting paid more than $125,000 a year.

The group’s name may sound familiar: It was started by Andrew Cuomo himself in 1986, and he headed it — at one-tenth of Belinsky’s salary — until President Bill Clinton tapped him for a Cabinet post.

He was succeeded by his sister, Maria Cuomo Cole, as unsalaried board chairman. Also on the board are Cuomo’s campaign treasurer and health-care advisor.

And it turns out that Belinsky’s wife is Lisa Vecchio — the governor’s cousin. Belinsky himself was once an aide to the governor’s father, Mario Cuomo.

All very convenient, we’re sure.

After a series of exposés, including by The Post, of nonprofit groups supported by taxpayer funds with high-priced CEOs, a newly formed Cuomo administration task force started sending out letters seeking detailed salary information.

The letters carried a suggestion of further, unspecified action in cases of excessive compensation.

Among the first recipients of those letters was the Metropolitan Council on Jewish Poverty — which exists largely thanks to taxpayer funds provided by Assembly Speaker Sheldon Silver and his allies, and whose well-paid CEO is married to Silver’s chief of staff.

Officially, the governor’s office said he was unaware of Belinsky’s resignation. And a spokesman for HELP insisted Belinsky’s resignation was unconnected to the Cuomo task force probe.

But the governor is famously aware of every sparrow that falls in Albany — and it’s hard to imagine this one fluttering to earth without Cuomo’s prior knowledge.

Which is encouraging — for it suggests that the not-for-profit probe will be anything but routine. No wonder that some nonprofits are genuinely concerned about what’s about to be uncovered.

Certainly Belinsky’s resignation sends another signal — that those who may be enriching themselves in the name of charity are now on their own politically.

That’s also to the good.