You and your family are in my prayers. You’ve received some good feedback so far. As others have said, until someone has reached the age of reason, canon law (and the obligation to attend Mass) doesn’t apply. Not that we want to leave our kids at home until they turn 7, of course. But there is no sin in leaving him home at his age—and that’s apart from considerations regarding his autism, which would only increase the situations where missing Mass would be okay.
I have a son with autism, too. He’s 9, but I would be hard-pressed to say he has reached the age of reason yet (it’s hard to say as he’s non-verbal). He hasn’t received his First Communion yet. Mass can certainly be a challenge. We make it through by sitting in the cry room. For him, it helps him to have a “spot” wherever we go. When we go somewhere unfamiliar, he seems to look for a spot he can walk back and forth in until that becomes his place of familiarity amidst the unfamiliar.
I really don’t like sitting in the cry room. My goal is eventually to get back in the main part of Church. That will involve some re-training of where his “spot” in Church is. We’ll most likely have to bring him in multiple times when the Church is empty. We’re still working up the courage to make that step.
I want to encourage you that our autistic children have a place at Mass. Don’t ever let anyone tell you differently. Certainly, for your own sanity and peace of mind, keeping him home when necessary is understandable. You do what you have to do. But don’t let anyone make you feel like you shouldn’t bring him to Mass. Jesus wants the little children to come to Him. That includes those with special needs. Even when they are being a bit challenging.