Here's some thoughts.
As gimel says swing the meds between morning and night. Either thyroid at night - calcium day - or vice versa.
I'd make sure whole heartedly that your 4 calcium/parathyroid labs are normal and lab test often while supplementing. You should have a calcium (ionized) - calcium (serum)- phophorus and Vit D panel ran recently. Often the Vit D is low and increasing that hormone (Yep Vit D is a hormone not a vitamin) can lower or entirely get you off the calcium supplement altogether.
Meant to answer your question - I take my Armour thyroid in the morning as early as possible. Then I busy myself for awhile (check email, etc) while I brew a small pot of coffee. I try to get at least 45 minutes to an hour before I have the coffee with non-dairy creamer. I take my calcium/magnesium at night before bed (its supposed to help with sleep)
I would not take Fosamax unless you have severe osteoporosis and there is no other way to impede bone loss. These drugs do not build bone but rather interrupt the natural bone rebuilding process (osteoclasts & osteoblasts) These drugs add a sheath or layer of hardening substance to the bone that impedes "loss" of bone density. However, in the process, it stops the bones ability to absorb calcium.
There are new studies that show the risks of bisphosphonate drugs. They include pssible femur fractures, esphagal cancer & osteonecrosis of the jaw bone.
If you are interested in investigating more about thse drugs that claim to build bone density Google this site: "Save Our Bones".
There are FDA warnings concerning Fosamax, Actonel, Boniva etc.
Most doctors are now told to recommend usage for two years or less - I spoke to my gynecologist about it - he was aware and in agreement about the new concerns. You see, it takes years for drugs to be on the market before the damage can be evaluated. Now my endocrinologist says I am in more danger of a fracture. (5% chance) Well, to me that means I have a 95% chance of not having a fracture.
Google "Fosamax & lawsuits" - I'd really think about natural remedies before going the Fosamax route. Reduce intake of acidic foods that leech calcium from the bones - take organic calcium (green calcium) higher doses of D3, magnesium, exercise...your body will respond!
Nothing wrong with taking T4 meds at night, unless it bothers your sleep. In fact there are suggestions that it can be a better time to do so. Here's a good link about that.
http://thyroid.about.com/od/thyroiddrugstreatments/a/bedtime.htm
I have this same dilemma. I can't believe there are not any answers here. Please respond.