I'd start now. She should be sort of thinking about where she'd like to attend from an educational standpoint so junior year can be about visiting schools, the SAT, and getting ducks in a row to apply.
You also need to decide if she would like to factor cheer into their choice of schools to consider.
There are 2 types of kids:
1. Ones who think about where they want to CHEER and select schools to visit based on that.
2.Ones who think about where they'd like to attend SCHOOL and then look at cheer programs at those schools.
I'd recommend number 2 but there are some kids who let cheer guide their college decisions. And that's fine too as long as you know that you will not be cheering 24/7 and that you may actually hate the school outside of cheer.
Some other things you can start to think about:
What are my strengths and weaknesses in cheer?
Do I want a coed or all girl experience?
Do I want to compete? Do I want to compete UCA or NCA style?
How do I feel about gameday? Do I want a huge D1 game day experience or something a little less intense. Also, consider that if you "hate cheering games" college cheer may not be for you. Unless you're cheering club, games are part of it. If you absolutely hate cheering games, but want to compete, you may want to research Acro and Tumbling.