That's a totally fair question! I can understand why that may seem like a fine line to walk; expressing happiness about that kind of thing could definitely be easily misinterpreted. Thinking about it, I'd say that one would start by NOT committing the list of faux-pas that I've seen often, e.g. OP's comment, stuff like "clever girl!" or really, anything placing a boundary between a woman into tech that you're talking to and that nebulous set of "other women", "the typical woman", because that doesn't exist in the first place (it's a social construct which encourages sexism). Here's a link I read recently which I agreed with wholeheartedly (http://the-toast.net/2015/04/01/things-male-tech-colleagues-have-actually-said-annotated/) Now, those are the most obvious ones, of course. But there are other things you can do as well!
Openly supporting initiatives to encourage women (or girls) into tech is a big one. Supporting your female colleagues when they speak out against sexism is also a big one. It means a lot when we talk about this issue and have male colleagues acknowledge problems. I've worked with some incredibly supportive male colleagues in the past, although some institutions are much better at this than others.
But if you're asking specifically how to say that you're happy that more women are getting into STEM, I'd say just what you said, that you're happy that more women are getting into STEM. A lot of progress has been made to break down barriers which discourage women and girls from these fields, and it's awesome when other people recognise that, especially when they also recognise that there's still a lot of progress to be made! I guess the difference between "I'm happy to see more women getting into STEM" and a sexist comment is where you place the blame for the discrimination in the first place. If you say stuff like "Wow, you must be [special in some capacity] because other women can't\don't do this", it comes across as a lot more sexist than commenting, e.g., on how it's nice to see tech being more female-friendly than in previous times, or stuff like that; acknowledging only the first-layer issue, which is that most women don't go into a STEM career, sounds like it's placing the blame on the women, rather than the system which is shown to impregnate girls with doubt into their own abilities from a young age, and which tends to pigeonhole us (men and women alike) into gender-specific interests and careers.
Honestly, I definitely see where you're coming from, and in this particular line of conversation, it's super easy to accidentally say something that can come across as sexist, even if you don't mean to.
I definitely encourage people to ask and listen to their female colleagues (like you're doing here).