I think the most effective way would be to show you're interested, explain what trans is, offer reasonable solutions yourself just in case they have no policies-offering solutions yourself will make it less likely that they'll just say "oh, we can't have a girl uses the men's room!", conclude by reinforcing your interest and asking for a copy of their policies, then give your standard closing line.
An example (that surely needs a lot of work, but here's a start):
Dear [Insert name]:
Nice little intro
I am greatly interested in attending your school [insert some reason if you feel like sucking up such as " due to your reputation for tolerance and diversity" or "great math program"]. Despite my enthusiasm, I have some concerns and I hope that you would be able to take the time to answer my questions.
Tell a bit about yourself, and offer solutions that way they don't have to be troubled to think of something
I am a transsexual male, which means that although I was born female, I identify as male and I plan on eventually changing my gender. [You can even add something like "Being addressed as a female causes me great discomfort...."] I would like to attend your school as a male without any of the students knowing that I was born female. This could be accomplished if I was allowed to be called by my chosen name, and have my chosen name be listed instead of my birth name on the attendance lists. Many transsexual males use the men's restrooms without problems, but I could use the restroom in the nurses' office if that would be against your policies. [If you know of any schools that have accomodated trans students, write a little about what they did here]
Reinforce your interst and ask about their policies
I would like to attend your school, and I feel strongly that I would excel in your program. If you have policies regarding transsexual students, could you please send me a copy? If you do not have any policies, I feel strongly that if we work together, we can come up with satisfactory accommodations.
If you have any questions or concerns, please feel free to contact me at [blank].
Thank you/Sincerely,
X