Matt,
It would be tough for me to do a fully accurate personal ranking for NJ because I haven't played some of the very good new courses like Bayonne, The Ridge,Trump Nat'l and Atlantic City post Doak. But...
When I see a course as good as Mountain Ridge ranked #17, I see a flawed ranking system. The fact that Forsgate(Banks) and Essex County are not on the list while Pine Hill and Shoregate are, further exemplifies my point. I feel the much the same as you do about Somerset Hills, I like the course a lot and while there are some great holes I've never held it in as high of a regard as most do. Unfortunately, technology has really hurt SHCC from a length perspective.
For rankings, the same would be true for PA. I haven't played most of the courses in Western PA, but I've played enough courses to question how Huntsville can be ranked as high as #5 and ahead of the likes of Saucon Valley, Huntingdon Valley, Lancaster, Philly CC, should I keep going?
Ok...I'll try. My top courses in NJ that I've played are:
Pine Valley
Ridgewood
Plainfield
Mountain Ridge
Galloway Nat'l
Baltusrol Lower
Baltusrol Upper
Hollywood
Somerset Hills
Hidden Creek
The next level would include Metedeconk, Forsgate, Essex County, Tavistock, Rock Spring, Montclair. I'm sure I'm forgetting others.