E.B.
First and foremost, it's a school. Ask what curriculum they use, whether the teachers are certified, what education/degrees/experience the principal or headmaster has. Google their curriculum and review it. For the older students, is the school accredited (and not just by some frivolous accreditation-sounding organization, but by a recognized accreditation group. You'd be amazed at what some schools pass off as "accredited". Yes, we're accredited by the Private Accreditation Company of the World Association. Uh-huh. You send them money and they mail you a pretty accreditation certificate. No questions asked!).
Second: Safety. Go and observe the drop off and pick up times. Are they chaotic, or orderly? Are the children supervised? Ask about fire drills and the policies about letting visitors in. Are doors locked and visitors ID'd? Is the building monitored and properly licensed by the town/fire department etc? What are their general student safety policies, both concerning any normal childhood playground accidents, and also bullying and illness policies? Ask to see the public record of any violations. How are their employees' background checks done?
Third: what are their goals for the children? Some schools want compliant behavior, some want academic excellence, some want athletes. Some want well-rounded students. Some just want your tuition and for enrollment to increase. If you plan to keep your son in this school for his elementary years, what are their educational plans? What kind of behavioral standards do they have and how are they enforced? What punishment plans are in place (demerits, staying in for recess, extra homework, etc).
Fourth: ask about extra-curricular activities, before and after school care, lunch service, transportation, sports, whatever is important to you. If your son needs any special services or has medical conditions, ask how those kinds of things are handled.
Fifth: find out if there are any restrictions on religion (if it's a religious school) or parent volunteer-time and donation expectations, or restrictions as to absences or other things that are important to your family. Some schools are very strict and will not tolerate absences due to occasional vacations, etc. Ask about dress codes, hair style restrictions, etc.
Just observe when you're there. Have a notebook and pen to jot down questions that come to you when you meet with them. Observe how open they are. If they're willing to let you quietly step into a classroom unannounced to observe a class in session, that's a good sign. If they only let you see prearranged set-up scenes, that's not.
Hope that helps.