Hi Burnham,
I think Stephanie is correct. You and your wife have to be consistent, as well as any human beings who your puppy is around with (your 9 mos old son might be difficult though
).
Dogs and kids are genius when it comes to find out who has looser boundaries so your puppy has figured out that he could get away with certain behaviors from your wife. My husband is less strict about "on your bed" command when we eat so our dogs try to lie down under the table with a hope someone drops some food, instead of being on their beds and stay lie down. I always have to correct their behaviors and make sure they are on their beds so that we can enjoy our meals even when we have company.
Another thing you can do is, based on your comment that your puppy recognizes that you are the Alpha (I personally don't like the word, I would rather say "the leader") and listens to you, you can help your wife establishing her position (facilitating her).
In other words, when you see your puppy jumping on her or doing something unacceptable to her and/or to your son, YOU can reprimand your puppy as the Alpha that YOU expect a different behavior from him to your wife. This will become very helpful especially when you add another family member or bring another dog/cat/animal to your family. From the very beginning, you teach your puppy how you expect him to behave toward new addtions.
I believe dogs will understand what is precious to you once you establish a trustworthy relationship with them. I bet you are already doing this but, for example, when your toddler is around your puppy and the puppy tries to jump on him, you would stop your puppy and reprimand, right? You can do the same with your wife. Of course your wife should be consitent with you.
Good luck
