As far as natural treatment for hypothyroid (I am assuming it is hypo- and not Hyper-) you could try glandular supplements and base the amount to give on what is said on the bottle for a human and back it down to dog size. A good brand is from Premier Labs (Raw Thyroid) as they use only organically rasied New Zealand animals. You could also try to feed your dog some kelp.
If there is any way to switch you dog from the commercial food to feeding only raw natural meaty dones and small amounts of raw veggies and fruits, this could make a 180 degree difference in your dogs' overall health. The cause for most animal ills is feeding a commercial pet food diet...
Sorry to hear you have tried so many things for the ear infection and nothing has worked.
Have you tried going to a holistic vet? They can guide you in the raw feeding and offer much help with the thyroid and ear infections.