I have to go with the Holy Hamptons Triumvirate, and not at all because I'm a native New Yorker (I've never played any of them, although I walked Sebonack for the 2013 U.S. Women's Open and NGLA for the 2013 Walker Cup, and, in addition to a lesson on the driving range, have gazed longingly at Shinnecock for years). By contrast, I played both Spyglass Hill and Pebble Beach (on the same very-expensive day) this summer and managed to snap a few pictures of Cypress Point while I was in the neighborhood. I was slightly underwhelmed by both courses.
My principal rationale is that the Hamptons Three provide the purer golf experience--fewer houses, fewer cart paths, more isolation. (Although I'm all about public and public-access golf, the privacy of all three Hamptons courses rids them of much of the commercialization that somewhat taints at least Pebble Beach and Spyglass Hill.) Assuming we're comparing the two sets of courses only in warm seasons, I would say the weather in the Hamptons is also more consistently better. Finally, the Hamptons Three provide the better variety: NGLA is as fun as they come (though I've heard the same about Cypress Point, albeit less so), Shinnecock is as "championship worthy" as they come, and Sebonack is the perfect mix between the two. I know Pebble Beach has plenty of championship chops, but I think most professionals would admit Shinnecock is the better championship venue--and course. And Spyglass Hill has a bit of an identity crisis.
FWIW, even by pure rankings, which none of us agrees with, the Hamptons still win, although it's admittedly quite close (the difference accounted for entirely by the difference in each set's "weak link"). Based on the latest Golf Digest rankings of the Top 100 courses in the United States, the Hamptons win 50 to 58 (lowest aggregate wins):
Shinnecock=4
NGLA=8
Sebonack=38
Hamptons Total=50
Cypress Point=3
Pebble Beach=7
Spyglass Hill=48
Monterey Total=58