I suggest you start here:
Typically, math is going to be a strong major at all kinds of colleges. Is she looking for a technical institute? Those tend to be more stem focused, but not necessarily the best option for a trans student.
It might be helpful if you could be more specific. What is her major? Is autism a big issue in her functioning? There are a lot of people on the spectrum who don’t necessarily need special support. Given the grades for her first two years of college, it seems academics aren’t the biggest issue. If support for autistic students is a must, along with being LGBTQ-friendly, you are looking at a more limited list. If the priority is to find a place where she can make friends and be accepted, focus on that first.
You said smaller, but UCSB and RIT aren’t necessarily small.