I have some specific experience with this, as I am in college right now and transitioned before I went. You're in the same position I was in a year or two ago. My advice is to apply as a female, then tell the college you're transgendered and ask them to change your records. My college did just that, and now all my records--and my student ID, which serves as a useful photo ID so I don't have to show people my female ID--say Andrew.
You definitely should apply to a GLBT-friendly school--most schools on the East Coast are very open and will accept you as you are. You needn't be "out" to everyone--I'm not--but you'll inevitably have to tell some school administrators, and definitely the health center. Your SAT scores, health records, and transcript will all be in your old name, but most people never see those, so you should be nice and stealthy.
I wish you good luck on your transition! I hope it doesn't interfere too much with your academic life--keep those grades up, buddy.
P.S. Apply to Williams! They're awesome!