Your puppy wants to be with the rest of the "pack" at bedtime. This behavior is highly adaptive from the standpoint of dog behavior. When a puppy becomes separated from its pack, it will whine, thereby allowing it to be found and returned to the rest of the group. This is why so many books on puppies and dog behavior strongly recommend that you allow your puppy/dog to sleep with you in your room to reduce the likelihood of crying at night.
Try moving the crate into your bedroom. If your puppy whines, first make sure it doesn't have to go outside to eliminate. This means getting up and taking it outside. If it whines again, or doesn't need to go outside, TAP your hand on the crate door and say something like "NO, SLEEP" or "NO, QUIET". If the puppy continues to whine, try giving it a toy or chew toy and then simply ignore any continued whining. If you don't reinforce the whining by comforting it (other than to take it outside – which is OK), it will eventually learn to settle down. Also, be sure to have a vigorous play session JUST BEFORE you are going to go to bed. This should poop it out, and it will sleep much more soundly.
Alternatively, you can designate a spot for your puppy on the bedroom floor. Keep the door closed or put a leash on it to keep it close to the bed. When it whines or moves about, take it out to eliminate. Otherwise, as above, say "NO, SLEEP."
Puppies that cannot sleep in the bedroom for whatever reason may be comforted by a ticking clock nearby, and a t-shirt of yours from the laundry.
Puppies want attention. They will do a lot to get that attention – even if it is negative! Thus, if you scold your puppy for doing things you don't want it to do, and ignore it when it is being good; you are reinforcing the wrong things. Ignore the bad things (or stop it without yelling or scolding) and enthusiastically praise it when it's doing what you want, even if it's as simple as sitting and looking at you, or quietly chewing one of its toys. This can be difficult to do, as it is essentially reversing all your normal reactions. But it is very important: you will wind up with a puppy that pays attention to you and is happy to do what you want, if it understands you.
It is essential to puppy-proof your home. You should think of it in the same way as child-proofing your house, but be more thorough about it. Puppies are smaller and more active than babies, and have sharp teeth and claws. Things of especial concern are electric wires. If you can get through the puppy stages without having your pup get a shock from chewing a wire, you are doing a great job! When puppy proofing your home, get down on your hands and knees (or lower if possible) and consider things from this angle. What looks enticing, what is breakable, what is sharp, etc. The most important things are watching the puppy and, of course, crating it or otherwise restraining it when you can't watch it.
Another step in puppy proofing is house proofing the puppy. Teach it what is and isn't chewable. The single most effective way to do this is by having a ready supply of chewable items on hand. When the puppy starts to chew on an unacceptable item (be it a chair, rug, or human hand), remove the item from the puppy's mouth with a stern, "NO!" and replace it with a chew toy and praise the puppy for playing with the toy. If you are consistent about this, the puppy will get the idea that only the things you give it are to be chewed on! Don't stint on the praise, and keep the "No!" to a single calm, sharp noise – don't yell or scream the word.
It is essential for every dog, no matter how big, or small, or whether you want to show, or work, or just play with, to have basic obedience training. If you want to go beyond the basics, that's great. But at least do the basics. One way to think of it is that without basic obedience, you and the dog don't speak the same language, so how can you communicate? But with basic obedience, you can tell the dog what you want it to do, and it will understand you and do it. Another way to think of it is getting your dog to be a Good Citizen: it doesn't jump on people, or run off, or indulge in other obnoxious behaviors – because it knows what you expect of it.