Stewart is accusing his deceased biological father, Earl Van Best Jr. The vice president of a cleaning company has compiled his account into a book published by HarperCollins.
"The Most Dangerous Animal of All" reveals Zodiac's true identity for the first time, the publisher says -- a claim Perez, Kaufman and others will likely dispute.
Stewart sleuthed for a decade through government files and news articles and hunted down relatives to dig up evidence, HarperCollins said.
The result is a narrative story about a "boy with disturbing fixations," who can't process being jilted by prospective mates and lets out his rage in a spate of murders.
Kaufman has described going to similar lengths with his obsession that his father could be the real killer. He even hired a handwriting analyst to compare his father's handwriting to letters the proclaimed mass murderer mailed to the press.
But since Stewart's account is new, investigators may take a gander at it to see if it helps them solve the case that is still open.
The author -- who was abandoned as an infant by his biological parents, then later adopted -- promises to answer questions in the case that have been open for nearly 50 years.
Police in Northern California have said they weren't aware of the book or its claims.
"It's an open and active case, so we don't comment," San Francisco police spokesman Albie Esparza told CNN. "But (it's) certainly something our homicide investigators will take a look at."
The Zodiac Killer stalked his victims with knives and guns in 1968 and 1969 and once even dressed as an executioner.
He craved publicity, taunting police in letter after letter to newspapers. The letters were often written in a cipher he seemed to have invented himself.
"If you read these letters, he was getting a tremendous thrill out of terrifying the public," said Susan Morton, a forensic scientist who has studied the letters.
The Zodiac's last known victim, San Francisco cab driver Paul Stine, was shot to death in his cab in 1969.
The killer cut out a piece of Stine's blood-stained shirt and mailed it to a newspaper, along with a letter.
Police believe the killings stopped, but the letters kept coming until 1974.
In the 1970s, a man named Arthur Allen was a prime suspect in the case. He was never charged and denied being the Zodiac Killer until his death in 1992.
Stirring the pot
As exciting as Stewart's account sounds, it may be just a new drop in the bucket.
More than 2,500 other people have been considered suspects in the case. Investigators said that for decades the phones rang regularly with people wanting to pass on new clues.
"We have talked to many people over the years," Steve Blower of the Napa County Sheriff's Office said.
Only two people are believed to have survived Zodiac's attacks. One was Bryan Hartnell, who was stabbed eight times in an attack in September 1969. His girlfriend was stabbed between 10 and 20 times. She died, but not before giving a description of her attacker.
A sketch of the suspect emerged, and HarperCollins says Stewart's father was a match for it.
"If you look at Gary's photo next to the sketch of the Zodiac (Killer) next to his father's mug shot, you can see that there is very clearly more than just a passing resemblance," HarperCollins publicist Tina Andreadis told the magazine. "They look alike."
Hartnell told CNN on Wednesday that he took a look at a head shot of Van Best that the publisher is circulating. That portrait is part of the new book.
"The things that I saw that were not inconsistent were the high forehead, the shock of dark hair, and the fact that he wears glasses," Hartnell said.
Hartnell has his reservations about Stewart's new account, but says he's interested in seeing the book.
"I somewhat follow the news, but there has been no time in the last 40-plus years when someone was not (stirring) the pot," Hartnell wrote to CNN in an e-mail.