Just because this is a family business does not mean that you have to put up with monkey business from the owner's son. You should treat Junior as any other employee, and if you are going to discipline him, make sure that you are applying the same standards that apply to everyone.
It sounds like you are afraid of the owner's reaction as a result of this discipline. If he somehow sides with Junior on this matter, he has clearly decided to run this operation as something other than a business. This type of a reaction not only weakens the character and skills of Junior, but it also weakens the character of the company in many important respects.
At this point, your job is to run your department as effectively and productively as possible. If you allow Junior to play the family card and get away with all sorts of nonsense, it is just a matter of time before the rest of your troops start to resent him and you.
In a word, Junior needs to be disciplined. If Junior's dad gives you a bad time, then this is a good time to look carefully at where the company is going and determine whether you want to go there with it.
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