While joint pain often indicates arthritis, joint/muscle pain is also a very common symptom of hypothyroidism. The fact that your pain is so bad, indicates that your thyroid medication may not be adjusted properly.
What thyroid tests do you have done on a regular basis? You should be getting TSH, Free T3 and Free T4. If you have current/recent test results, please post them here for us to see. Be sure to include reference ranges, since those vary lab to lab and must come from your own report.
Do you know if you have Hashimoto's Thyroiditis? It's the most common cause of hypothyroidism in the developed world.
What thyroid replacement medication are you taking, at what dosage?
Pain in the joints sounds as though it might be an arthritic issue unrelated to your thyroid issues or thyroid medications. Before this joint pain gets any worse it might be advisable to get a rheumatologist on the case, or at least consult another general practicioner or internist.
Do you take any anti-inflammatory over the counter medications for the pain? Of course you should consult your doctor about this first.