I played both on consecutive days in January. Deciding between the two is a nice problem to have.
Pine Barrens is a more challenging course, I believe, if only because waste areas tend to include other elements (e.g. grasses, bushes, trees, and the like) while similar areas at Dunes were simply sand (with some exceptions).
Dunes #17 is an interesting hole, but is utterly defenseless without the green. It's not nearly as strong as a couple of Pine Barrens' reachable par fives (like #4). Dunes #18 was a very good hole, I thought, what with the centerline bunkers and putting surface and all.
Possibly OT: Dunes gets a huge nod when one considers value; we played Pine Barrens on a day when $165 was the going rate, while Dunes was around $40 the next day. If the two courses were remotely comparable (and they are much more than that), I'd head to the Dunes for that difference alone.
WW