I will be getting out of the U.S. Army in a few months.I will be enrolling in an online college to complete my bachelor's degree in criminal justice.There are thousand's of excellent schools available.Each school claims to be the best for my education.What questions should I ask the registrar's office so that I can narrow my choices and choose the best school for me?

I would start with some review sites like this:
StudentReview.com (http://career.studentsreview.com/)

You can find more review sites here (http://www.google.com/search?num=100&hl=en&lr=&safe=off&q=reviews%22online+colleges%22+OR+%22online+univer sities%22&btnG=Search):

They will give you some good stuff to think about - and ask individual schools - when you're narrowing it down.

Kaplan, AIU, Univ of Phenoix and FMU are some of the good online schools in criminal justice.

You may wish to find something at a local college, since you will also get some crime lab and criminalists classes that are just not possible online.
Also many colleges ( not all of course) have internships with local police departments that are very helpful.

But having been lin law enforcement for many years, I know that the schools I listed (and there are others to) are well accepted. But remember no one department will view any school the same.
And actually if you want to get into law enforcement, ( I have to laught) many departments prefer degrees in management ( esp if you want promotions latter) degrees in accounting, and languages and computers help if you want to go to work for federal law enforcement