I think you are right. You should pay the most attention to the sub-field rankings. I've noticed that many of you are applying to MPP programs. The programs at the top of the MPP rankings are no surprise. Berkeley, Harvard, Chicago, Princeton et al. are all there. That said, if one is interested in nonprofit management, then one should move away from the Harvards and Chicagos and look at Indiana, Minnesota, NYU, Washington, and Syracuse.
This is just dumb and doesn't deserve a response. When you design and administer your own survey, you will understand.
You are right. An academic reputation survey will most likely lead to somewhat different results. Practitioners will value some different things. Regardless of whether you are going into academia or a public service job, these rankings are not a bad starting point.
However:
If you want a PhD in Public Policy, shoot for Harvard, Michigan, Chicago, etc.
If you want a PhD in Public Administration/Affairs, shoot for Syracuse, Indiana, Georgia, etc.