Mr Freeman previously said he would cremate Manson and spread the ashes, putting to rest "this so-called monster, this historical figure that shouldn't have been blown up as big as it was for all these years".
The dispute over the body foreshadows a similar fight over his estate in a Los Angeles courtroom.
At least five people had petitioned to take possession of Manson's body since his death at age 83 on November 19.
The case in Kern County was brought by the coroner's office, which said it wanted to quickly resolve the matter because bodies were piling up at the morgue from the methamphetamine and opioid epidemics.
A vicious court battle over his corpse ensued, with three supposed heirs to Manson fighting for the fate of his body. He said Channels had used his contacts with Manson to generate memorabilia to pay his mortgage while also denigrating the killer in conversations with others.
Manson's body has been the subject of a legal battle with numerous people contesting they should be given the body, including Freeman, another man claiming to be Manson's long lost son and a prison pen pal. "I'm irate. That Jason Freeman, he just pulled the wool over the whole system's eyes".
Michael Brunner, 49, whose birth certificate lists Manson and cult member Mary Brunner as his parents, was also in the fight.
Charles Manson talks during an interview August 25, 1989.
"Freeman is hereby determined to be the surviving competent adult next of kin of the decedent".
Freeman claims to be the son of Manson's son, Charles Manson Jr., who later changed his name to Jay White to avoid association with Manson. Lentz claimed that Manson fathered him during a Wisconsin orgy and was named as the sole beneficiary in a 2017 will that the cult leader apparently signed.
Knight noted that the will did not appear to be properly executed and that Lentz forfeited his claims as an heir because he was also adopted. "No sufficient probative evidence was provided to this court to refute Freeman's claim", Knight said in her ruling.
Some adversaries have suggested others want to profit off the death by selling morbid photos of the corpse to tabloid publications.
To prevent photos of the body from being leaked, the coroner's office stored Manson's remains under a pseudonym and only two employees were told its true identity, Walters said. A video online shows Freeman's son playing with a Manson puppet, complete with swastika on the forehead, and Freeman joking about stuffing the doll with Manson's ashes and taking him fishing.
Most of the people vying for the body have said they would cremate it, though Freeman and Channels balked at that suggestion when Deputy Kern County Counsel Bryan Walters suggested having the coroner cremate the body and allowing the parties to continue their court fight over the ashes.