If your doctor is dosing your thyroid med based on TSH, then it is very likely that you are hypothyroid and that can cause joint pain like you mention. TSH is a pituitary hormone, not a thyroid hormone, and it has only a weak correlation with the biologically active thyroid hormones, Free T4 and Free T3, and has a negligible correlation with symptoms, which are the best indicator of thyroid status and are the patient's concern. A good thyroid doctor will treat a hypothyroid patient clinically by testing and adjusting Free T4 and Free T3 as needed to relieve symptoms, without being influenced by resultant TSH levels. Symptom relief should be all important, not just test results.
You can confirm what I say by reading at least the first two pages of the following link, and read more, if you want to get into the discussion and scientific evidence for all that is recommended. Note especially Rec. 12 and 13 on page 13 of the link.
http://www.thyroiduk.org/tuk/TUK_PDFs/The%20Diagnosis%20and%20Treatment%20of%20Hypothyroidism%20%20August%202017%20%20Update.pdf
So you are going to have to convince your doctor of the need to test as recommended in the link, and then treat clinically as needed to relieve symptoms. If you have trouble with the doctor, give him the link and ask him to read and reconsider clinical treatment.
Also note that hypo patients are frequently deficient in Vitamin D, B12 and ferritin. If not tested for those you should do so and then supplement as needed to optimize. D should be at least 50 ng/mL, B12 in the upper end of its range and ferritin should be at least 100. All 3 are very important for you.