The career criminal accused of fatally shooting the 12-year-old son of a retired NYPD cop pleaded not guilty Thursday — as the boy’s heartbroken mother fought back tears just feet away in a Bronx courtroom.

William Ferrer, 45, clad in beige jail scrubs, entered the plea in Bronx Supreme Court in the July 25 stray-bullet killing of little Jacob Freytes, who was caught in the crossfire outside a Mount Eden bodega.

Jacob’s mom, Migdalia Martinez, dabbed her eyes with a tissue as she watched Ferrer in court for the first time, surrounded by about a dozen family members.

“I just wanted him to see how I felt, what he left me with. I feel like a…

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