So I've been friends with a girl for 16 years. She's my best friend, but we don't talk very often (we're both pretty quiet, but we live close to each other)

I have no idea how to tell her. I mean, what am I supposed to say? "Hello heterosexual female friend whom I've seen in her underwear, I'm a guy. Please don't have your boyfriend punch me, he's considerably larger than I am"?

Under normal circumstances, I think she'd be cool with it... except it might come up that I can out to a different friend over a year ago since I was switching to the same college and I didn't want her to out me.

I've been putting this off because I don't know what to say... but I really think that's just making it worse.

Any advice? Tips? Absolutely-do-NOT-dos?

I would say face-to-face, but that's me. You ask her to go out or something, -i can only assume she has no problem with gays or trans folk, and knows what trans is-, so just dive straight into how you feel. 'I've been meaning to tell you something, but i have been putting it off as blah-de-blah, i know i am a guy, and i am doing blah-de-blah to organize myself. I've told my parents, their reaction was _________/I have yet to tell my parents as ________. Do you have any questions? I am sure she'll ask if she does. Also, be honest with her, tell her why you told your other friend and not her. Don't hide that from her if she does not know, as if she does find out, it could cause a situation.

I was in a similar situation, only my best friend and I have been friends for 25 years and I live now in another country than she does, so we see each other only about once a year face to face and the rest is on skype and phone.
I also told another friend of mine before I her, because I knew it would be easier for me, since that friend is Genderqueer and went through similar issues as i have.
Anyway, I talked to my friend on skype and simply told her everything- starting with being a boy in childhood and having problems with my mom because of it, how it continued to push me into denial for many years, and that's why she never heard about it until now..to how it came up again in the past few years and the change in my life since she saw me last.
I must say she took it very well! better than expected. I said I hoped that she can get over the shock and see me in time as the guy that i am and she said she loves me as I am, woman or man, that she always saw me as a boyish type so it's not such a big shock and that I should have no worries about our friendship.

I guess my point is- simply be honest and explain how you feel, why it took you a while to come out etc.
She's your friend for many years..although it might come as a shock to her, she might also see things that in retrospect would more sense to her, knowing this.

I would say you should tell hell her like you would any girl. You would be surprised at how she might react in such a positive way. Even more so because she's your friend

I did the same thing this past week. I just gave a brief rundown of when I started noticing things were different and went straight to the point. She was shocked as I was always a "manly man" as she put it, but she said she was honored to be the first person I told. She has asked a few questions every day which is good because it gets me to thinking about different aspects and views from a woman's perspective.  I wish you all the best!!