Toughest course, I'd probably vote for either Olympic or Bethpage. Not only are they both long, very long, but Bethpage has drastic elevation changes on nearly every hole, IMHO. And it been a while since I've played a full 18 at Olympic so I can't remember if it has those nasty ups and downs too, but I'm guessing it probably does. Also, at Bethpage it seems like nearly every hole is a dog leg, so even if you hit the fairway off the tee, there is no guarantee you will actually stay in the fairway.
And as for the hardest hole, I have to go with the Par 3 13th at Olympic, for a myriad of reasons. The pin placement is so tricky that you have almost no green to work with. And if you come up short, you're on the beach facing a tough up and down. Not only that, but any tee shot that misses long will have an EXTREMELY nasty break to deal with. Its almost a guaranteed 3 putt -- at least it is for me anyways. I've parred that hole maybe 3 times in my entire life LOL. I'm sure it doesn't help much that a) I've only been on tour for 1 month, b) my starter putter sucks, c) my starter WGT unlimiteds suck, and d) I absolutely suck at putting overall, but right now I think this is the toughest hole for me.
And a close runner up is number 17 at Royal Saint Andrews. The length isn't really that bad since I have a legit driver and 3 wood, but the fairway is so darn narrow that I almost always end up in the thick rough. From there, its basically a hit 'n hope punch 3 iron on a wing and a prayer that it finds the second level of the green, or at least gives you a good lie to pitch and putt for an up and down. Even if you do find the fairway, the green is so narrow that attacking the pin is highly risky, especially with the large bunker if you leave it short. If you are unlucky enough to land on that first level of the green, its basically a 1 stroke penalty IMHO. I've had countless rounds that have singlehandedly gone from pretty good, not bad to son of a #$%^& all because of that one hole.