my sister has the same issues with her chow mix. She never used a crate before and her dog just got totally anxiety prone practically overnight. The trainer she had said to buy an airline crate rather than a wire crate. She tried prozac for her dog but it didn't work.
I would not leave a water bowl in the crate and I would cover it as others have suggested. You might consider putting it in a place where your dog can't see out into the backyard and potentially see squirrels so as not to excite the dog. A good chewing object (bone, kong etc) is a good idea to keep your dog busy while you are out too. Hope you can get things to settle down. Good Luck