Great topic. A good place to start looking at data is IHSAA enrollment numbers and then John Harrell’s website on the “combined yearly records” page. Going back as far as the data goes, which is 1984 here are the results.
The smallest schools on the list are Linton, Eastbrook, and Tipton. This data speaks volumes for those programs. To be in the top 20 in winning percentage of all schools in Indiana in the last 38 seasons, is quite a statement. I imagine a lot of people will argue for Mater Dei, Andrean, and Chatard, but there is no way a private parochial belongs in this conversation, ever.