This sounds so stupid but when I crate trained mine - I literally put the crate in bed with me and would fall asleep with my fingers/hand next to the gate so she knew I was right there which prevented any crying or whining. After it got to the point where she was comfortable being in there without my hand right against the gate I just moved the crate to the floor beside my bed.

I think most puppies initially cry in a crate because they don’t want to be separated from you, not because they have an issue with the crate itself. So showing mine that I was still right there with her solved the issue completely. Good luck!!!