First, check you scenery.cfg file and locate Imagine Sim's KEWR entry and check that it contains the exclude switch: Exclude=N40 42.50, W74 09.27, N40 40.26, W74 11.58, objects. If not, place this under the listing and check to see if this eliminates the default buildings.
If they still exist then use Airport Design Editor and place an exclude rectangle over the area where the buildings are. Also, make sure there is not duplicate AFCADs for the airport. That should eliminate it.