Hello and welcome..
There could be many reasons why your puppy is waking up, barking and whining. I am guessing he is trying to tell you something!
(1) perhaps he needs to relieve himself?
(2) perhaps he is spending too many hours in his crate? What's the puppy's daily schedule? Is he bored?
(3) perhaps the puppy is hungry? How many times a day is he fed and how much are you feeding him? If a puppy's belly is full, they are usually content.
(4) perhaps he does not want to be alone? Labs are people dogs and don't like being away from their family members.
(5) perhaps he needs a Vet visit. Is it possible he's in pain or is there something wrong?
These are just some ideas I am thinking of...hopefully, others will chime in.