I am the non custodial parent (father) of a 5 year old son in Boston. Recently I was offered an amazing job opportunity in Arizona. My sons mother and I do not have a court ordered agreement as of right now. What are the chances I will be able to bring him to AZ for visits during school vacation? And can I still try for joint custody over state lines?

Obviously you can't have joint physical custody, but no reason you can't have joint legal custody.

And, if you can show you have been an active part of your son's life, I see no reason why a court won't grant extended visits over school holidays. Such visits will probably be at your expense, however.