Very good question James.
First off, both of these courses are extremely good. I would cry like a little girl if I could join any of these two. But that being said, I would have to go for Friars Head.
Why Friars Head? Mostly because of a few little (and I do mean little) things that Sebonack has going against it, IMHO.
Things like a first hole that doesnt seems like it fits with the rest of the golf course. The obtrusive presence of a few condos overlooking that first hole. Two man made ponds that look like they don't totally fit there. And finally, a few holes that left me somehow indifferent, although they would be great probably anywhere else (Namely, 13, 15 & 16).
On the other hand, Friars Head has a few things going for it as well. Things like a routing that is simply inspired. An interesting mix of holes and settings. A great practice area and a nice practice course. And finally, the absence of any condos, roads or any development that intrudes in the course. All this gives you a feeling of being alone in a golfing heaven.
In a few words, that place seemed just perfect to me.
Anobody should jump on a chance to play any of these courses. But if I had to choose, again, it would be Friars Head.
YP