There are a few references to it being on the second floor of the caves; for example: Chapter 2d - Spring 1228 - A Visitor From Afar
Also, Stephen's lab is noted as being on the first floor (Vacant and Guest Laboratories), and I'm fairly sure we didn't have both of the storerooms turned into labs (because one of them was being used as the infirmary up until relatively recently when a dedicated building was constructed for it).