|The term "healthy disagreement" can be translated to mean "major argument," and it's rarely a good idea to engage in these with anyone, especially the owner's son.
And speaking of the owner, one important question is whether he emphasizes the first or second word in the term, "family business." If he is running the operation as a business, you should be able to approach him and have a businesslike discussion on the issue behind your disagreement with his son. In such a discussion, keep the subject focused on work issues, and not on his son.
However, if the owner is focused more on family than business, then you have a larger problem. When business decisions are made more on the basis of bloodline than product line, it can be dissatisfying for the employees and destructive for the business. If this is the context, you have little to gain by discussing the matter with the owner.
Either way, the best approach over the short term is to try to distance yourself from the owner's son. And over the long term, you may need to distance yourself from the company.