My lab did the same thing. Here s what I did.
The crate was in the dinning room. I would take her out for airing than put her in the crate. I covered the crate with a light blanket making sure there was air spaces. When she cried i would go out and lay on the floor with my fingers through the wire. She would lay down against my fingers and go to sleep . I would than sneak back to bed.
When she was 4-5 weeks home. I would get up if she was yelping for no reason and shake the kennel. A week of that and quite all night.
The next challenge was in the crate in my car. She would howl the whole time I was driving. After about 3 weeks of that .i got up one Sunday am put here in her crate in the car and drove around the block at 5mph. every time she made a sound i gently bumped the brake just enough to make her fall.
1 hour later she was silent and never made another sound in the crate.
She is so quite that a couple times I have forgot she was there.
Do what works but never beat up on them. And try to use methods they do not associate with you.