Matt,
From my perspective, Bayonne is an engineering marvel, and in many ways, it's a tremendous and exciting golf course. I'm fairly certain that Eric Bergstol got what he wanted out of the design, which is very high on visual dramatics.
I wouldn't rate it as high as you have it, however. I can't imagine what the average score is out there, frankly, and given the wind conditions, I question the narrowness of a number of holes, I question the length and thickness of the fescue surrounds, and I most seriously question the wild undulations of the greens.
Most links courses tend to have more subtle, sedate greens, and that's for a good reason. While I know The Old Course has wild ones, there is also enough width and playability to land a large jet. At Bayonne, the exactitude required by the severity of the hole locations borders on overkill in any kind of wind.
All in all, it's a really fun, exciting course and brutally demanding. I'm also betting that it could host a US Open, and in that regard, I believe it's more difficult than Whistling Straits. Still, I can't imagine playing it every day, and most of the courses in my top 20 don't share that caveat.