I'm not sure where you're researching to find that Levothyroxine has an adverse effect on bones. That's not true. Everyone needs thyroid hormones and when the body doesn't make enough, we have to get it somewhere else - Levothyroxine, in some form) is the # 1 prescribed thyroid medication on the market.
We don't know your age, but hypothyroidism can have an adverse effect on bone density in children.
In adults, over-treatment (high thyroid hormones), specifically, with high Free T3, it's the high level of thyroid hormone can be detrimental, not the levothyroxine you're taking.
There could be a lot of reason for ankle/knee pain - including hypothyroidism which causes bone, muscle and joint aches/pains, along with many other symptoms.
If you would care to post your most recent lab results (you should be getting tested for Free T4, Free T3 and TSH on a regular basis), along with their corresponding reference ranges, we'd be happy to provide further insight.