Here are things I'd suggest you consider. Many come down to personal preference (no right answer for everyone) but think about what matters to you. These things are in no particular order, except maybe price.
1) Price: This includes tuition, cost of living, length of the program, other freebies like do you get free access to a school gym or do you have to buy certain equipment/technology.
2) Clinical affiliations: How do clinicals work? Are they interspersed in the program or all at the end? Are there part time and full time? Don't just go by the list of any affiliation, see if you can get a list of where students are right now (just because a school has an affiliation does not mean they frequently get spots there). How are clinicals decided- is it a lottery, do they make sure you get your top pick(s) at some point? Are clinicals local or scattered around the country?
3) Class size/demographics. Some people like big, some small. Pros and cons of both. Are students generally fresh from college or older. If you are older, you might not want to be surrounded by 22 yr olds. Where do the students come from? If you are coming from far away and everyone else is local, this might make it harder to establish yourself in a social group.
4) Location: goes with price/cost of living. If you hate cities, probably don't live in one. If you have a favorite hobby, make sure it is still accessible. How much will it cost you to visit friends/family? Will you have to commute a long ways?
5) Curriculum: How is the curriculum structured? Is it team based/problem based learning or more traditional lectures. How are labs done? Is anatomy prosections or dissections. Is there a heavier focus on ortho or neuro? Do you do all basic and then clinical courses, or is it a mix? Is there required research project? What about breaks between semesters?
6) Faculty: Are faculty involved in APTA? Involved in research? If you have a big interest in peds, for example, see if there are faculty doing peds research. Do you have opportunities to work with the faculty on research? How are clinicians utilized in teaching labs? Are the rest of the faculty more clinical or academic?
7) Access to clinical populations. Do they bring in people with stroke, spinal cord, ortho injuries, etc for hands on practice in classes? Is there a school associated clinic?
8) What are the extra perks? Does the school support you to attend CSM (big meeting)? Some do financial support and scheduled time off. Do they pay your APTA memberships? Career fairs? Help with networking? Provide board prep classes? Is there a residency program associated with your school?
9) Boards pass rate. You want it darn near 100% if not 100%. Or they better have a good reason why!