Depends on how you want to approach future planning. Are you alone in managing all the domains? Are/Will there be others that will manage those schools? If you're alone, probably just having the one domain and add subdomain's for the separate schools might be better.
But if those schools grow and you require to expand, in the future you may want to purchase separate domains for those schools.
We have a small school separate from the main school that has its own domain, but could still function just fine with a subdomain.
I work in a small school setting (200 users) and have 4 domains (but we pretty much just use the 2, one domain set for students, and 1 for Staff)
Our separate school has its own domain, which helps to make it unique website and separate from our other schools.
It all comes down to what you see happening in the future.