Why can't it be Unplottable just because it's surrounded by Muggles? If the wizards were there from the beginning, they could have made it Unplottable and cast Muggle-Repelling Charms which over time cause it simply not to be noticed.
In Book Three of Alexandra Quick, it will be seen that San Francisco (which is a fairly small and very crowded city) actually has an extra hill that Muggles don't know about, because wizards settled there when the city was still new, and put charms on it to keep Muggles from noticing. It's possible that if Muggles were specifically looking for terrain features that have somehow gone unmapped, they could do a survey and realize something isn't quite right, but why would they?
Now if you want wizards to arrive and just suddenly stick a secret magical school in the middle of a metropolitan area, that's more problematic. In that case, I'd say they have to create a plausible facade for it, backed by spells that prevent Muggles from questioning the external appearance or investigating further.