I have primary residential custody of my son, but joint parental responsibilities. I sent my son on vacation to be with his mother in Venezuela for the summer. My Ex wife never sent him back and his passport expired while there on vacation, it's been 2 yrs since he has been home. My question is can I go to the embassy in
Venezuela and renew his expired passport being that we have joint parental custody, but I have primary residential custody of my son.

No, your son has to go in person with either custodial parent, currently biometrics required.

My son is going with me, the question is if my exwife has to be there? Thanks