Having studied the list closely, and recognizing that there are many courses on it that I've not played (yet), my opinions are as follows:
WFGC West is an excellent, excellent course, but I have to go w/Shinnecock as #1.
Baltusrol Lower ranked higher than NGLA? The major championship thing must count a lot on this ranking. B'rol is a good course, but National has more architecture/per hole than most any place on earth.
Quaker Ridge "only" #6? Lots of architecture there, too; better than WF West to many; hard to argue either way, IMO.
Garden City #7? I can't get enough of GCGC's ambience and the good holes are wonderful. It deserves a high rank just for having no halfway house (some would remove the drinking fountain near the 10th tee, as well), but is it better golf architecture than WF East, B'rol Upper and Friar's Head? I can't get there from here.
Fisher's Island #8? Like Garden City, another all-world golf place where the good holes are uber-excellent. But better golf architecture than Friar's Head and WF East? I put it just ahead of GCGC (personal taste) but not those other two.
Stanwich as high as #13? Would it really rank that high if 10 of the 18 greens weren't ungodly fast?
Stanwich ahead of Friar's Head??? No chance, no way.
Friar's Head behind Stanwich, Fisher's and GCGC? See above.
Maidstone below Fisher's Island? That's a tough call, but I call them even (also personal taste).
Piping Rock below Somerset Hills? Somerset is like Garden City and Fisher's - I'd play there every day if I could (Piping, too), but Piping has more appeal to me even after some of the "improvements".
Baltusrol Upper only #26? It's way better than that.
Montclair Golf Club barely in the Top 50 and, also, ranked lower than Deepdale? MGC deserves better than that.