Federal authorities gave long-time government mole John Thomas a Good Friday surprise, arresting him at his home early Friday morning.

Thomas, who was a major player in the investigation into political fundraiser Tony Rezko as well as former Ald. Ike Carothers — including wearing a wire to record conversations — allegedly stole $370,000 from the village of Riverdale in tax increment financing funds connected to the development of Riverdale Marina.

A three-count indictment unsealed Friday alleges the real estate developer, 51, used the stolen taxpayers’ money to repay personal loans and debts, legal fees, rent and other personal expenses.

The money was meant to be used to renovate the Riverdale Marina, where Thomas’ business, Nosmo Kings LLC, kept an office.

But in 2012, Thomas created fake invoices for non-existent companies and for companies that never performed work at the marina to fraudulently obtain reimbursement from the village, the feds allege.

Thomas’ connections at the marina included several shady figures, the Sun-Times has previously reported. Thomas in 2012 purchased an $8,350 money order for Raghu Nayak — the convicted healthcare fraudster and political fundraiser who allegedly offered former Gov. Rod Blagojevich a $1.5 million bribe to appoint Jesse Jackson Jr. to the Senate — for “plumbing work” at the marina. Thomas allegedly owed Nayak, who does not appear to own a plumbing company, $17,000 in unpaid rent at the time.

And Regina Evans — the disgraced former Country Club Hills police chief who was convicted of state grant fraud and has been linked to other alleged scams — and her husband both worked at the marina, sources said.

Former Riverdale Mayor Deyon Dean, whose administration presided over the marina fiasco but also filed a lawsuit against Thomas in 2012 accusing him of fraud, welcomed Thomas’ indictment Friday.

“When you do inappropriate things, it comes back to haunt you,” he said.

“We tried to work with Mr. Thomas in good faith — he was a convicted felon, but he had purchased a business, and we thought we could move forward with him.”

Each of the three counts of wire fraud Thomas faces carries a maximum sentence of 20 years in prison.

Wearing a gray fleece and jeans, Thomas pleaded not guilty during a brief appearance before U.S. District Court Judge James Zagel Friday afternoon.

At the hearing, prosecutors alleged Thomas’s wrongdoing went well beyond his actions at the marina, urging Zagel to keep Thomas locked up while he awaits trial.

Thomas has carried out five additional financial scams since the 2012 marina plot, including trying to pay his former lawyer’s bills with fake Babe Ruth baseballs he bought on eBay, Assistant U.S. Attorney Sunil Harjani said.

But Thomas’s new attorney, Lawrence Beaumont, said Thomas has been in negotiation with the government for months. He accused prosecutors of improperly trying to “send a message” to Thomas by attempting to keep him from his family over the Easter weekend.Speaking outside court, he said Thomas had paid him with “money — trust me, I wasn’t paid with baseballs.”

Zagel said he was concerned that Thomas might try to take more money if he is freed on bail, but would rule whether Thomas can be released later Friday.

In the meantime he ordered court staff to check if all the phones and computers in Thomas’s downtown condo can be removed or monitored, to prevent Thomas from communicating with the outside world if he is allowed out under house arrest.

The hearing marked an unhappy return to court for Thomas, who in 2010 escaped prison time and instead received three years of probation in Chicago’s federal court for his role in a scheme tied to his days in New York.

In a 2008 interview with the Sun-Times, Thomas said his life had become “frantic” as he amassed hundreds of hours of recorded conversations for federal investigators while trying to maintain the real estate business he had built over time.

For a time, Thomas helped investigators build a record of repeat visits to the old offices of Rezko and former business partner Daniel Mahru’s Rezmar Corp., at 853 N. Elston, by Blagojevich.

He worked to rebuild his reputation in the years that followed, though several high-profile deals he was involved with fell through.

In 2008, he told the Sun-Times he was glad he was getting a second chance in Chicago, telling a reporter, the city “is a wonderful place to do this kind of business. It is the most forgiving.”