Yale does have the best non-profits program in the country, that said, all 3 of these schools admit the vast majority of their students as general MBA applicants (not non-profits specific which is a small niche), and it is true, you are comparing apples and oranges here (H/S attracting a different applicant pool entirely vs Yale SOM). Whatever your GPA, your chances of getting into SOM will be VASTLY greater than they would be of getting into H or S. It's true that all 3 of these schools give a lot of weight to GPA, but at H/S you will be competing with the best of the best - many students who apply to only H/S, or some combination of H/S/W/K/Chi/MIT, and have stellar work experience, GMAT's and GPA's. At Yale SOM you will be competing with people who are applying to the higher ranked schools above, but don't get in, as well as a lot of people who apply to mainly Cornell, Michigan, Duke, Darden, CMU, etc. Far less of these people are going to be the "total package" (super high GPA, GMAT and great work experience). So you've definitely got a much better shot there.