Your TPO antibodies are causing the hives. Supplementing with thyroid hormones should eventually put them to bay, but it could take a long time. You should try to reduce the titer of antibodies by taking a selenium supplement every day, up to 200 mcgs. Larger vitamin stores/departments carry it. If you take a multi-vitamin, check it for content and take it into account in the 200 mcgs/day total. Selenium has been shown to decrease TPO titers up to 40%.
It always amazes me what doctors don't know.
An allergist
might have more knowledge about the TPO/hives connection, but there isn't much more to be done about it even if he/she does know. Trying the selenium and waiting for the antibodies to leave is your best bet.