First of all you kick ass for taking this kind of interest in your niece!
Finding support groups isn't always easy, especially when you don't live near a major city. While "legitimate" support groups like you may find at centers (although I've never been to one) may have the most appropriate setting, other trans women are not always the best people to seek support or advice from. I'm sure I'll get some flak for saying this, but it's true that not all trans girls lead sane, stable lives. She should be careful who she lets into her life.
I'll do some research and ask around on my own... there should be one in Richmond at least but I suppose that's a bit of a drive. Maybe you could drive her to one or two meetings? It may help her make at least a friend or two from the area. Most TG groups only meet once a month anyway.
Does she have a therapist yet? This will be the first step in her transition. It's not just a good idea, it will be necessary to clear any roadblocks for her down the road. If all else fails, I have a number for you but she will only be able to do sessions over the phone.
What else, what else? XD The mom is going to be a bit of a problem, but it's not an uncommon situation. Is planning on starting college any time soon? College is a fantastic environment to transition in. You're away from home, with none of the same pressures. You have a much more accepting environment. And she'll at least have the opportunity to meet more of her peers.
Speaking to her insecurity, by the way, this is completely natural! I was a lot like her when I grew up. Now my friends can't get me to shut the hell up XD. Once she becomes secure and confident in her identity, more and more of her will begin to come out. But it's going to take time. And unfortunately...
Transition SUCKS. It sucks BIG TIME. Yes, yes I know it's a "beautiful time of change" when a girl can "finally be herself" but the reality is it's one of the hardest things a person can ever do in their life! It takes patience, discipline, iron will, and more heart than most people have in a lifetime. There will be many nights of sadness and desperation. Times of feverish anxiety. It may seem to her like she's trying to accomplish the impossible.
Long story short, the night will be long before the dawn.
Just keep reminding her that dawn is there! No one's usually around to pat us on the back and say "You're doing a great job" or "You look better all the time" but this is exactly what she'll need.
She should have a plan of action. Timelines aren't important, but should feel like she's making continual progress. tsroadmap.com is an excellent resource for the practical things she'll need to do if she's not aware of it already.
Plans aside, if you'd like to support her, then please keep encouraging her! Let her know when she's getting closer to her goal. If her voice sounds better, let her know. If she loks beautiful that day, tell her. Those words of encouragement do more good than you may realize =).
I'm not sure how close you two are, but if you can...help her. She may feel frustrated with makeup, unsure of her style, or generally uncomfortable with her new role in the world. If she hasn't gone out presenting as a woman yet, go out with her. Pick a calm, comfortable setting and go out for just a few hours =). My first time was to sit down at a restaurant for just a few hours and have a pizza =)! Try to make it a positive experience and it will serve to reinforce her self-esteem and commitment to transition.
More than anything help her keep up hope! She's still very young, so she may get lucky with a short transition (6-12 months) but for most of us it can takes years (1 1/2 for me but that's very, very lucky)... typically it takes 3-4 years at least.
Don't let her give up her dreams. Nothing is impossible. I've known girls that made it through situations that would *destroy* most human beings

.
Just let her know how proud of her you are and that you accept her as your niece and things will be fine =).
And, of course, feel free to have her contact me if she likes =). I'm a 31 year old trans girl from North. Cali. I finally finished my own transition about 3 years ago but the experience is still fairly fresh in my mind. Every one of us has a different experience with transition but sometimes it helps just to have someone you can vent to =).
Thank you for being such an amazing person Maxie!! =)
-Kelly