menstrual problem--thyroid? PCOS? post-pill?

Double posting this in the women's health forum too.....
I am a 32 year-old woman, just over 5'6" and 125 pounds.
Here is brief but concise history of  my problem: I went on the pill at 19, as at that point I had only had a few periods in my life (they ran some tests at that time though I can't remember, and I believe they found nothing wrong). I was an athlete (runner and swimmer) so I'm guessing that had something to do with it--and may still.
I just went off the pill in July of this year and had a period five weeks later (which has always happened when I went off the pill accidentally, on a vacation). Then I had some spotting ten weeks later. Since then nothing. So it's been about five months.
I had some blood work done last week as I was concerned about this. Most levels were fine, though my TSH was 3.74 with free T3 of 3.5 and free T4 of 1.0. Prolactin was 10.3. Let me know if you want to know about others, though the nurse's said most all else was in the "normal" range.
Anyway, my TSH was 3.2 in April of 2011. I am wondering if my amenorrhea is possibly due to my thyroid, as my TSH has gone up quite a bit in 1.5 years, and I know that now many doctors consider 3 to be the cut-off. My sister also has some slight thyroid problems and is on a low-dose of L-thyroxin for it.
Side note-- I am a pretty serious runner, though have not run nor exercised in the past month because I was hoping my periods would return. They haven't.
Could it be PCOS? Thyroid? Do I just need to wait? Is it because of my exercising? The doctor  who did the blood work said I can't exclude that it's still post-pill amenorrhea, but I basically feel that there might be something bigger wrong with me, especially since I was having problems at 19 before the pill. I am not underweight, and I enjoy running, so I want to be able to continue to do it. I also want to be having my period!
Finally, if anyone has advice about the type of doctor in NYC who might be able to treat what might be complicated to diagnose, could they please let me know?
Many thanks.