DY,
My guesstimate would be around 7-8k per student. Although I admit that I have no clue how much utilities/maintenance/insurance cost for a school building.
CTLawyer,
Out of town yeshivas have significantly fewer students compared their in town counterparts, so things like the Rebbe’s salary is split among 10 kids as apposed to 23+.
Also find me a NYC yeshiva which has grass, so they save some $ here too 🙂