I would also consider the possibility that he’s cold - sleeping alone, even at room temperature, is not what a young puppy would choose. I would definitely think about using a hot water bottle and/or getting a heating mat (that they can sleep on OR next to OR choose not to sleep on as well…make sure not to cover the entire bottom of a crate with one).
It is a big stretch to expect a young puppy to go from a litter and mom to sleeping alone in a crate away from its “people.” Obviously people do this all the time and eventually they figure it out, but it’s not pleasant at first.
We always kept our puppy crates in our bedroom so that the puppy knew we were there. One puppy was a big cry baby and got invited into bed fairly early on; the 2nd puppy was the best crate sleeper and was dead to the world from 9:30 to 5:30am every single night; and the 3rd puppy slept ok in the crate, but tended to move around a lot, make a lot of noise, and did some whining (and got invited into bed pretty quick too).
In retrospect, I think puppies #1 and #3 might have been cold - we got one in November, and the other in March. When we invited puppy #3 in bed with us, he slept on my head, and put his nose in my ear. I think he really was cold unless he could snuggle up with something.
Not everyone likes a bed dog, so if you do not - I definitely suggest finding some for it to snuggle with at night.
And yes, crate training is a great thing - even if your dogs sleep in bed. It makes so many things so much easier if your dog enjoys being in a crate – dog shows, trips in the car, dog classes that are long enough to have a break. I love having a dog that is good about crating.
Good luck!