Please correct me if I am wrong, but my impression is that most "mainstream" economics programs are now focusing less and less on economic thought history. So, in order to do research on economic thought history or some comparative studies on economic development, perhaps history department is a better place to study? What are some good programs for that? Thank you!
What are some good Phd or research programs for Economic History / Economic Thought History?
The RePEc/IDEAS website publishes various rankings in economics. I would suggest checking out their ranking of authors working in Business, Economic & Financial History or History & Philosophy of Economics and see if there are people that you'd like to work with. Usually you can find a list of recent publications or working papers on their website/CV. See if any of those are to your interest. The ranking of departments in those fields (HIS, HPE) may also be relevant.
In addition, there are specialized journals for the fields you mention, such as the Journal of Economic History and Journal of the History of Economic Thought. Their recent publications should give you a sense of who's currently active in those fields and what they are working on. Also, papers on economic history do get published in mainstream journals. You should be able to find them by searching for articles with the appropriate JEL codes. In your case, codes "B" (History of Economic Thought, Methodology, and Heterodox Approaches) and "N" (Economic History) are relevant.
There is also "A Guide to Graduate Study in Economics: Ranking Economics Departments by Fields of Expertise". Table 3 in this article ranks economics graduate programs in the US by JEL codes. Keep in mind, however, that this is a 13-year-old paper. So information therein may not be up to date, since people may have moved/retired/etc.