I'm not 100% sure that I agree with two parts of your sentence! The part you are asking about is easy to resolve. "Stand out in" is much better, since you express that she is particularly noticeable for it, rather than "better than" which indicates that being healthy is some sort of competition or graded event.
The other part that has caused me some issues is "you are healthy". Being healthy is a state of being and is somewhat a case of luck (someone with a nasty disease versus someone without). Consider that you perhaps want to say something like this:
One of the things you stand out in, compared to any other girl, is the fact that you lead a healthy lifestyle.
One of the things you stand out in, compared to any other girl, is the fact that you live healthily.