I know I'm late to this thread but I only just stumbled upon it. The simplest solution is to simply crate you pup.
Start off teaching him that the crate is amazing, throw treats in there to teach him that good things are in the crate. Once he's happy going in then you can start closing the door, reward him when the door is closed and then let him out(do this with increasing duration). you can even feed him in his crate too so that he associates it with all the good things in his day to day life.
Doing this training over the course of a day 5-10 minutes at a time will have him ready by the night time to relax and go to sleep. Pop him in the crate, close the door, maybe give him a stuffed frozen Kong to keep him busy and then go to bed. if he cries ignore it. It's not cruel because you know he's safe in there, you know he doesn't need the toilet because you've done your usual night time routine, so the crying is because he wants attention but h needs to learn he doesn't get it by crying.
When you come down in the morning, let him out and give him a big fuss then carry on with your usual routine.
This is what we did with our now 11 week old pup and she goes in her crate at 10pm ish then I go to bed, a member of the family puts her out for a wee around 12.30am and she sleeps through to 6.30am
we started putting her out at 1am and again at 4am and slowly moved the 4am one back to 3.30am etc
we also feed her in her crate and in the morning she is sat waiting gets let out for toilet and then runs back into her bed waiting for her first meal