Here is a list of PT programs that use the PTCAS application process. If you click on the school it will tell you whether or not they run a masters or doctorate program. There are other universities not using the PTCAS application as well.
www.ptcas.org/DirectoryByState.html

Masters or Doctorate?
The masters programs are being phased out in the U.S. Soon all PTs will need a doctorate to practice in the US, and I anticipate this will make it more difficult for visiting physiotherapists to find work. If you have a choice, I'd recommend the doctorate. The programs are virtually the same with the exception of a few more units in the doctoral programs.