This was a difficult decision for me, too.
I had a single nodule on my right thyroid lobe. Over the course of three years, the sonograms showed it was growing, but the biopsies were "inconclusive." My blood tests were always completely normal--they usually are with nodules, cancerous or not. My doctor advised me to have my right lobe removed, despite the fact that we didn't know if it was cancerous or not. After a lot of research and asking my doctor a thousand questions, I had the surgery. It was cancerous. A month later I had the other lobe removed, then I had radioactive iodine treatment, and have been cancer-free ever since (that was three years ago).
I won't tell you what you should do, except to tell you to do a lot of research and ask your doctor questions. Does he or she want to take out your entire thyroid, or just one side? You can function perfectly well, sometimes without thyroid replacement medications if are able to keep half. If you aren't satisfied with your doctor's answers, get a second opinion before you decide to disregard his or her advice.
{One question: are you saying that your nodules are goiters or do you have both? They aren't the same thing.}
Please write back about what you ended up deciding and how everything goes. Good luck.