What a pain in the butt...
I'm on the ususal regimen (spiro, estradiol, and progesterone), and started out paying for it myself. The estradiol and progesterone are cheap (I get them through my doctor's office and he supplies them at cost), but the spiro is pretty pricey, so I started putting that on my insurance. I figured that since it is prescribed to men for high blood pressure it wouldn't raise any red flags, and so far, so good.
You seem to be stuck in just the opposite situation; what really stinks is that if you were listed as male, there wouldn't be a problem! Could you switch to a different anti-androgen, one that is routinely prescribed to women? I think I remember hearing that spiro is sometimes prescribed for women with facial hair.
I would also check into the exact policies of the NY system to see if they specifically exclude medication for transgender issues. If not, a phone call may straighten out the situation. You may want to contact the Sylvia Rivera Law Project (www.srlp.org); they have a legislative initiative in the works covering some of these issues, and may be able to provide you with information.
At any rate, good luck!
Annie