It’s a miracle on 51st Street.
A 3-year-old boy reported missing in Florida two days ago was found safe and sound last night — in St. Patrick’s Cathedral.
The adorable child, Nathaniel Fons — who had been the subject of a frantic Amber Alert out of Flagler County — was in a car that mysteriously pulled up in front of the church at 6 p.m., police sources said.
He was taken out of the vehicle by a woman who walked him inside and told a security guard she needed to see a priest, the sources said.
The guard told the woman she had to go to the rectory.
The jittery woman then stuffed a piece of paper in the boy’s pocket and fled. The frightened, crying boy pulled out the note and gave it to the guard.
It bore the name and phone number of a Florida detective. The guard called the detective and the NYPD.
The Florida officer then faxed over a photo of the missing boy — and Nathaniel’s identity was confirmed.
“It’s been an emotional roller coaster these past two days,” the tot’s overjoyed grandfather, Donald Fons, told The Post from his Florida home last night.
Struggling to choke back tears, Fons, 57, described how he and his wife raised the boy they call Nathan until the child’s mom and their son, the boy’s dad, fled with him last August.
“It was total heartbreak, a total empty feeling when they left,” the emotional granddad recalled.
Fons said his son was jailed two months ago on an arrest warrant for a vehicle break-in, and Donald and his wife heated up their custody bid for the child last week — likely prompting Nathan’s troubled mom, Erin Comeau, 26, to launch the chain of events that led to the boy’s frightening disappearance.
Florida cops say Comeau was traveling with Nathan, 21-year-old transient Christopher Michael Brandstetter-Howell and another couple, Eleanor Black, 29, and William Scott, 32, and their two daughters outside Daytona Sunday night when Erin was nabbed for passing a $100 counterfeit bill trying to pay a $77 gas charge.
At the time, Comeau and Nathan were with Brandstetter-Howell in an RV reported stolen from New York. The other couple and their two kids were in a Chevy Suburban.
When she was arrested, Comeau told cops to allow Black — who Donald Fons said he believes is Comeau’s half-sister — and Scott to take Nathan, and couple was allowed to leave with him and their daughters.
The SUV in which they were traveling was later found abandoned in a hotel parking lot, after which police issued an Amber Alert for Nathan.
“It was just terrifying,” Donald said. “We found out he was missing Monday morning. . . . We told [police], ‘We have no idea who these people are.’
“The biggest fear was if someone tried to pull them over and if they were armed or gave chase . . . anything could have happened,” said Fons, a former sheriff.
As for his “very friendly, very playful” grandson being dropped off at St. Patrick’s, Donald said, “A church isn’t too bad.
“To tell the truth, I don’t give a darn where he was dropped off, as long as he’s safe.”
The child was taken to New York Hospital and found to be in good health, sources said. He was placed with Children’s Protective Services.
Meanwhile, NYPD detectives last night were scouring video at and around the church for clues to the car, which bore Florida plates.
“Thank goodness the people knew enough that St. Patrick’s is a place that a child can be taken care of and be safe,” said New York Archdiocese spokesman Joseph Zwilling.
Additional reporting by Erin Calabrese