Here are some suggestions:
ribosomes- the teachers (they do the work in making the products/outcomes of a school much like ribosomes make the proteins of a cell)
mitochondria- the boiler, mechanical, or electrical room of the school (where ever the main source of power is located). Or, you could to the lunch room- the source of energy for students and staff.
nuclear envelope- the main office- you must pass the main office to get to the principal's office (the nucleus).
vacuole- the school pool? A vacuole is made of mostly water.
endoplasmic reticulum- the hallways where people and things are transported throughout the school.
golgi bodies- this could be security or the person that greets and directs students and visitors. A welcome desk, if your school has one.
cytoplasm- everything inside the brick walls of the school- like the classrooms.
lysosomes- the big trash cans that the janitor puts the classroom trash in.
chromatin- something that is kept inside of the office that contains information; I would do either the lessons, worksheets, and other papers that students learn from (like the code to enable learning); or, the file folders/computer database of each of the students in the school.