I totally agree, except it's not necessarily time to get another boyfriend, but time for sure to get rid of this one.
If they can't get along when he's 9, it's going to get horribly worse as the boy gets older and more assertive in the teen years.
Your boyfriend and son have known each other for five years. They do not get along. Well - it's time to get another boyfriend as this relationship is already "failing". Sorry - but your son must come first.