Those buildings don't come with JFK, they are caused by another scenery in conflict. Try to use the free FSX Airport Scanner utility program, to see if there are duplicates AFCAD at KJFK.
If the conflict scenery is not an AFCAD, for example a Mesh or a Landclass add-on, then you must find it and disabled it on your own.
Of course, I assume you have JFK on top of the Scenery Library (or, at least, on top of every non-airport scenery you have), which is where its installer puts it by default automatically. If it's not, first thing to do is to place it back on top, and then try the other suggestions if the problem persist.
