He played 1 home game every 3 days with an average attendance of 5,000.
I think I should put a comma after "3 days", but I'm not sure.
Both with and without are valid in this case, so it’s a matter of style.
I like it better with a comma. Without the comma, someone might mistakenly interpret the “with” clause as applying to “days”. Adding the comma separates it just enough that it more clearly applies to all of the games he played.