First of all, keep in mind that I am unable to diagnose you because I am unable to examine you, this forum is for educational purposes.
Your symptoms are most consistent with cervicogenic migraine headaches (migraines that come from the neck). I do not think the levothyroxine is contributing to your headaches, but it is likely that your neck is undergoing changes after the radiation treatments that lead to muscle stiffness, pain and headaches. Other typical symptoms of migraine headaches include photophobia (lights hurt the eyes), phonophobia (sounds make the headache worse), nausea/vomiting and worsening of the headache with movement. Some other symptoms that can occur with neck related migraines include vertigo (room spinning) and imbalance. There are rare cases of seizures in the occipital lobes (back of the brain) that can cause flashing lights, but this is less likely. I would recommend a migraine medication such as a triptan (relpax, maxalt, zomig, etc). If you continue to have headaches you may consider a preventative medication such as elavil, topamax, nadolol etc. I would also recommend neck physical therapy and a muscle relaxor such as zanaflex. An MRI of the brain and EEG should also be done to rule out others causes (tumor, seizures etc).
I hope this has been helpful.