What are good PhD programs in Systems or Systems Thinking?

The downside is that there are not many Ph.D. programs solely focused on systems thinking/systems science, but the upside is that ANY Ph.D. program can be...

When looking for university-level training that is explicitly focused on Systems Thinking and Systems Science of various kinds, you'll find many individual courses,  dozens of Masters programs and a paucity of Ph.D. programs. Here are some of the Ph.D. programs that exist (their inclusion on this list does not constitute an endorsement):

Please let me know if you know of other reputable accredited programs.

However, if you are interested ins systems thinking/systems science and you want to do a Ph.D. nearly any Ph.D. program you find in any discipline or topical area will be amenable to a systems approach or lens being applied to your doctoral work. Usually these permissions are left up to your doctoral committee. And, usually your doctoral committee can be composed of between 3-5 members selected by you. Some of those committee members (not the Chair of your Committee) can be external members (outside the university), so if there are no specialists in systems thinking at the university where you are doing your Ph.D. then you can identify someone and have them installed as a member of your committee. 

Our advice:  If the above options for Ph.D. don't work for you for whatever reason, choose a great mentor who studies the kinds of things you are keenly interested in and apply to the program where they belong. Mention your interest in utilizing a systems lens. Add external advisors to your committee who have expertise in systems thinking as needed. We have assisted hundreds of doctoral candidates with this process.

Caveat emptor: Be aware that many programs will have their own "flavor" of systems thinking. This is especially tru of system dynamics and systems engineering programs. While this need not be a problem, it is something you want to be aware of. If you end up at one of these programs, make it your goal to leave the program "better than you found it" by exposing them to the many other flavors of systems thinking (i.e., See: Cabrera, D., Cabrera, L. and Midgley, G. (2021) The Four Waves of Systems Thinking. In, Routledge Handbook of Systems Thinking, (Eds) Cabrera, D., Cabrera, L. and Midgley, G. Routledge. London, UK.)