It really depends on what you want to do. I would argue the MBA is better for managers and directors (e.g. human resources manager, finance director, marketing manager, accounts manager) while an MPA is better for analysts (program analysts, policy analysts). The MPA makes program recommendations that the MBA would then implement.
I got my MPA, my friend got my MBA. He is having an easy time finding IT and network management jobs, I am having an easy time finding research and analysis jobs. When it comes to getting jobs with a non-profit, I think that, in general, MPAs are preferred, whereas in the private sector, MBAs are preferred.
The main difference between an MBA and an MPA is as follows: MBA = management, finance, and marketing, while an MPA = management, policy, and program development. As such, the MBA is better for the private sector, the MPA for non-profit organizations and government work.
What you need to look at when you choose your schools is what you want to do with your degree. Consider the following:
MOST IMPORTANT, even before I get to the numbered points: Accreditation. NASPAA for MPA, AACSB. Now, onto the list -
1) Cost - If you can't afford a school, you probably shouldn't go to it.
2) Research or Practice - Do you want to work in policy, planning, and development or do you want to be the one who controls the implementation of programs? If you like the former, go to a school with a thesis or cumulative project requirement. It will be a pain in the butt, but it will set you apart from the rest (maybe a polytechnic college like a Cal Poly SLO/Pomona or Virginia Tech). If not, go to a place where you can say screw you and just do X amount of classes to get your degree (like a UC Davis for an MBA or an NYU).
3) Full-time or Part-time - If you plan to work, you need to pick a program where you can be flexible. Some programs are lock-step, so you have to take certain courses at certain times.
4) Are professors readily accessible - If not, unless the program is online, skip it. Which leads me to my final point -
5) Format - Do you want a hands on program? And online program? A lecture based program? Do you want to learn from case studies? Do you want more theory or more real-world?
My International Relations BA + my MPA from Cal Poly Pomona = my working in international crisis analysis, making great money, and enjoying life. I am now applying for DPA programs at the University of Georgia and University of La Verne.