You need to submit a Proof of Citizenship application for your son and a separate PR application for your wife. If you include your son in your wife’s application - CIC will eventually kick it back to you and tell you your son is already a citizen and to apply for him via the correct methods. Each application requires different paperwork and evidence - so they can’t be combined.
I just wanted to add a follow up. I realized that I should not list my son on the IMM0008 form because it clearly says so in the document itself. I also talked with the call center and they advised that I can apply for both at the same time so that is what we’re going to do. Processing times seem to be about the same for both where we are so I think we should be good to go in about a year!