Grab a water bottle, squirt when whining and walk away. If the whining persists, spray again.
It took our pup 2 nights to understand we were not going to put up with the whining.
I also agree with a comfy bed liner. But I disagree with placing water in the crate. (to each is own) That will increase the nightly bathroom trips. Night time is the time for sleep, not drinking and restroom breaks. (again, just my opinion)
Also, a walk or jog before bed time is great. After we eat dinner, while the kids are cleaning up the mess, we take our pup on a walk with a backpack on that has 2 water bottles in it for extra weight to wear him down. We get home, he gets a drink and we let him out right before bed and all is well through out the night.
Best of luck