Persistent cough and occasional choking when eating...could this be thyroid or throat related? endoscopy and colonoscopy ok. lungs ok.

Not right: Something is not right. The simplest explanation is that you are getting food in your lung, you need evaluation for that by a speech pathologist. Certainly, that is not the only possible reason.

See an ENT doctor: This could be reflux esophagitis, but with neg endoscopy less likely. Esophageal diverticulum, or possibly vocal cord lesion or post nasal drip from sinus congestion are all possible. Could be thyroid but less likely without obvious neck expansion. See an ENT doctor. They may help with this.

Dysphagia: The symptoms you describe are concerning. The endoscopy can only tell you information about the anatomy and not about how the swallowing mechanism is functioning. A swallowing study (modified barium swallow study) may be necessary to figure out what is the problem. A formal swallowing evaluation would be important as well.