The answer will rely mostly on how old the puppy is. If it's really young it may miss it's mother. Put a clock where it sleeps maybe that'll help.
If it is older and you want the puppy to stop whining, we did this with our dog. Leave it be until it stops whining, when it stops and is quiet for a few minutes...then give the dog attention. If you give the dog attention whenever it whines, it's going to keep whining b/c you gave the dog a power.
My dog hardly every barks now, and only whines when she she needs to go outside or needs food. Good Luck with whatever you choose, it's hard to get through, but it'll be worth it in the end!