Pediatric endocrinologist is the best step. Your son needs to be put on thyroid meds since he is hypothyroid. Hypothyroidism can lead to mood irregularities and depression - combine that with puberty and it can be maddening (for him and you).
What type of thyroid cancer did your father have? There is a highly genetic form of thyroid cancer (medullary). If that is what your father had you and your son need to be tested for the MEN I and MEN II genes. Find out what type of cancer it was and let the pediatric endo know all of the details you can find.
While you are waiting for the referral ask your pediatrician to run a thyroid ultrasound and *complete* thyroid panel with antibodies. It could be as simple as an autoimmune thyroid condition or thyroiditis but it could also be more severe. Having all the tests run prior to the appointment with the pediatric endo could save you valuable time and make the first appointment more productive.
Here's some information about thyroid conditions that may lead you to more discussions with your son's doctors. http://www.endocrineweb.com/thyroid.html
I went through tough thyroid conditions (precancer) with my daughter too. Hang in there mom - sometimes it's harder on the parents than the kids. Oh, and it's okay to cry, freak out, ask questions, and vent here. That's what we are here for.
Utahmomma
papillary carcinoma '03, second surgery '04
recurrence and RAI '06 and '08
three sisters with papillary carcinoma (one with three recurrences)
other sister with precancerous thyroid
daughter with precancerous thyroid
I can't offer any help, but I just hope everything works out OK for him.