Make sure the puppy has an article of your clothing with him at night. I used to sleep with an old tshirt tucked into my bed so it would smell like us, and at night I would put it in with the puppy. I would put a new old shirt in bed with us so that we had another one ready to go if the first one got soiled and had to be washed. I found this helped the pups a lot. I also had the crates by the bed. I could drop my hand down for them to smell or lick if they got too upset. It didn't take long. I always checked if they were fussing too much to put them outside to potty, but once I knew they were okay, they were allowed to whine for a while. It wasn't always easy, but it paid off in the long run.
That said, years ago when my lab was a puppy the first couple nights of crate training were a nightmare and I put her in bed with me. It was perfect, she'd sleep right through. Whatever works. It is good though that he's used to his crate and eats in it. Just remember never to use it as punishment.