Tom Brady’s shenanigans with the football apparently date back long before Deflategate.

That was the allegation Wednesday from former NFL quarterback A.J. Feeley, who told a Philadelphia radio station that he saw Brady using a doctored ball during home games as far back as the 2004 season.

Teams had to use the same collection of balls on offense before the NFL — at the loud behest of Brady and Peyton Manning — changed the rule in 2007, allowing clubs to bring their own balls on the road.

Feeley, who last played in the league in 2011 with the Rams, was a backup with the Dolphins 11 years ago when he says he saw a Patriots ballboy sneak a special football for Brady to use in a game in Foxborough, Mass.

“I was on the sidelines and I noticed that somehow this beat-up ball from the ball boy was getting thrown in for New England, yet when we were on offense the orange brand-new ball was getting thrown in,” Feeley told 97.5 The Fanatic in Philadelphia.

“I even said something to the ball boy, and he kind of gave me a smirk. At the time I tried to address it with the coaches, but everyone was like, ‘Oh, that doesn’t make a difference,’ or ‘Who cares about that? You’re looking at some stuff that really doesn’t matter.’ ”

Despite the brush-off from his own coaches, Feeley said the incident bothered him and fellow backup quarterback Sage Rosenfels, who later spent a season with the Giants in 2010.

“Sage Rosenfels and I were on the sidelines and were like, ‘That’s crazy. He’s basically getting his own ball thrown in on offense,’ ” Feeley told the station. “That was an issue for me at the time. … We saw it then.”

Feeley was asked to weigh in after Brady was nailed by the NFL with a four-game suspension for being aware that footballs were deflated for him during the AFC Championship game and for refusing to fully cooperate with the league’s investigation into the matter.

Brady has asked the NFL Players Association to take the lead in his appeal, which the three-time MVP will try to get heard by an arbitrator without close ties to the league. Brady also reportedly has hired powerhouse labor attorney Jeffrey Kessler, who could try to take the league to court.

The choice of arbitrator is up to NFL commissioner Roger Goodell, though, and Goodell even could decide to hear it himself.

Goodell’s handling of the investigation by Manhattan attorney Ted Wells has come under fire from Patriots owner Robert Kraft, who blasted it in a statement Monday as “one-sided” and hinted that he might not accept the league’s punishment of a $1 million fine and the loss of two high draft picks.

Kraft is one of the most powerful owners in the sport and has long been a mentor and confidant of Goodell, to the point GQ Magazine reported earlier this year that Kraft’s nickname in the league office is “assistant commissioner.”

That relationship has been seriously strained by the Deflategate investigation, but Goodell appears to still have the strong backing of other influential owners.

Goodell and all of the owners will be attending the league’s spring meetings in San Francisco next week, and Cowboys owner Jerry Jones told ESPN Dallas on Wednesday that he still stands firmly behind Goodell.

“He’s doing a great job, and I’m a supporter of his,” said Jones, who added that “fairness” is one of Goodell’s strengths.