From About.com Thyroid forum
How to Take Your Thyroid Medication
1.Always check the prescription against what you receive. Don't allow generic substitutions.
2.Most doctors feel that taking thyroid hormone on an empty stomach allows for maximum absorption.
3.Many practitioners advise that you allow at least one hour before eating, because it allows for maximum absorption.
4.Be consistent about a high-fiber diet. If you start or stop eating high-fiber, get your thyroid rechecked, because it may change your absorption.
5.Many experts recommend you take vitamins or supplements with iron at least two to three hours apart from thyroid hormone. Iron can interfere with thyroid hormone absorption if taken too close together.
6.Be careful about taking calcium and calcium-fortified orange juice at the same time as thyroid hormone. Allow at least 2-3 hours apart, so absorption is not affected.
7.Don't take antacids within two hours of thyroid hormone. Allow at least 2-3 hours apart, so absorption is not affected.
8.Watch for interactions with antidepressants & thyroid hormone. Zoloft, Paxil and Prozac can make thyroid meds more or less effective. Talk to your doctor.
9.Don't stop taking thyroid hormone when you're pregnant or breastfeeding. It's necessary for you and your baby's health. Talk to your doctor about adjusting to the right dosage.
I am hypo from Hashimoto's thryoiditis and just had a total thyroidectomy. I take my Synthroid alone, in the morning on an empty stomach.
If you're taking it with anything else, you might not be getting full absorbtion of your thyroid medication. I'm on several thryroid forums (medhelp.org has a great thyroid forum and very active--you can always stop by and ask a question there or do a search) and have seen a lot of people say that they started taking their thyroid meds at night before bed, about 3-4 hours after dinner. The key is being consistent in whatever you do so that you are regulated and discuss it with your doctor.