I'm not sure what are good criteria for comparing schools. Test scores? Student/teacher ratios? Amount spent per student? What about a good elementary school that feeds into middle and high schools that don't seem as good? My son is only two and a half, so I'm obviously not involved in the local schools. But this is a really important part of our decision making.
As you have suggested, many communities have portions of their school system that are superb (e.g. K-6) and other segments that are poor (e.g. 7-9). I'd investigate whether the educational philosophies of school systems embraced teaching to different learning styles (auditory, visual, and kinesthetic) and whether they provided rich arts and music programs and individualized academic enrichment opportunities. Safe schools, a well-furnished and maintained physical plant, adequate recreational and sports facilities, and a well-staffed guidance department at all levels are a few more items that should be on your check list. I do not condone tracking systems in education but that is a personal and professional preference and may not be a concern to you.
It might help if you contacted the PTA's and PTO's in these towns and talked to some of their members - personal conversations with these folks who have kids in the school system might prove invaluable.
Good luck with your move and thanks for writing. I know that I have not provided you with every item of importance but I hope my suggestions were helpful.