Play Cuscowilla, but you are asking the wrong question, IMO. See paragraph three...
I have played both within the last 6 weeks, and as KBanks says, it ain't close. And I like Great Waters a lot! Cuscowilla is just a great, great golf course; a "modern classic", as Mr. McBride terms it, is NOT an overstatement.
I'll give you a heads up, though. If you are going to be in that area, make the effort to play a second round not at Great Waters but at Long Shadow. The back nine is now open, and you'll be able to tell people that you've already seen it when the course starts getting national attention, which will happen soon. In fact, if you have already played Cuscowilla, I would seriously consider making Long Shadow the one round choice. It is that good; wait and see.