Exton, Pennsylvania was not opened until the 1980s. The first actual station building is nearing completion.
The Downeaster stations are tricky. Although markhb rightly mentions Brunswick as a substantial new station it is located almost exactly in the place of the former Maine Central station site. The Freeport station likewise reuses real estate very close to where the "last call" was made by Maine Central on Labor Day weekend 59 years ago this September.
Portland is a relocation from the previous Union Station site nearby. Old Orchard Beach likewise is legacy or near legacy real estate. Same could be said of Saco. Wells on the other hand is definitely "new" and is sited for its proximity to the Maine Turnpike which was built some time after any station which may have served Wells at one time.
There is a proposal in the works for a West Falmouth station which to the best of my knowledge would indeed be "new" under the criteria of this topic (I'm assuming old flag stops dating back to the 1870s and 1880s don't count).
The New Hampshire stations are all near, in or next to their former Boston & Maine station sites. Likewise for Haverhill and Woburn as others noted. North Station never closed.