It sounds like pup was not properly crate trained, and its a little late to re bake that cake. So at this point, this is what you must do: (after you make sure he is not whining because of physical pain or illness....vet check..)
One: feed high quality dry dog food ...all he wants....in the crate (door open)at the start of the day...after fifteen minutes pick up the remainder and don't feed him again till the next day, same time, same routine, (in the evening you can give him a small (little) treat and of course water as he wants it)
Two: Don't let him sleep during the day, if he gets really tired show him this huge bone you got from the meat market just for this occasion (very little meat on it..its purpose is not food but to further tire him from all the work he is going to do to try to reach the marrow)....Hold the bone inside the crate so he has to enter the crate to get it...lie down outside the crate so your head or body is blocking his exit and relax, yawn and pretend you are going to sleep, if he is very tired he will be asleep soon...carefully remove the bone without waking him and put it back in the fridge leave the door open and go about your daily activities.
Three: At bedtime, put his crate next to your bed,cover it completely with a blanket and physically put the dog in without any coaxing, trickery etc. Just grab him by the rump of his tail push down on his head and put him in as fast as you must...Just make sure that when you say "place" his head is through the door..quickly shut the door, turn out the lights and go to bed.
DO NOT say or do anything that would give him the idea that you can hear his whines, screams, yodels, pretend chokes, etc....You MUST make sure he is really tired so he wont have the strength to whine all night....Also make sure he uses the bathroom before he goes to bed. make sure you SEE HIM use the bathroom, don't just put him outside and hope for the best. Follow these instructions TO THE LETTER! and you troubles will be over in two or three days. Good luck.
Psychology major, ex dog trainer, sixty-three years of life.
"Natural Dog Training" by Keven Behan
"Schutzhund!" by Susan Barwig.