Look at the dropout rates, the average number of years to PhD completion and where the graduates go after they get a PhD. Also look at the number of hours per week that are required by the program. Check how many students each professor has, and if he or she has time to help each student with research. See how many publications and presentations are completed by the average student in the program. Are the students happy?
My daughter had the choice between a couple of big state universities and a small program at a lesser known school. She realized that the small school had a lot of money, a high PhD completion rate, lots of publications by students, and happy students. She picked the small school and finished the PhD in 4 years. She is now doing a post doc at a big state school that is not very organized.
She should visit each school and really spend time getting to know the students.