Puppies whimper for many reasons, and while it can be cute for a few minutes, the sound of incessant whining gets old quickly. Still, whining is one of the few ways your puppy has to communicate. Don't discipline him for whimpering; instead, aim to understand what he is trying to say. Disciplining your puppy for whimpering can confuse him and make him timid.
Whimpering is a means of communication. Your puppy may be whimpering because he needs to go outside, he is hungry or thirsty, or simply because he is bored or lonely. Make sure his needs are met. If he has recently been outside and it's not mealtime, provide some active play or bring him onto your lap for a cuddle. It's always better to meet these needs before he starts whining, so he doesn't learn to associate his whimpering with getting what he wants.
While welcoming a new puppy into your home is a big adjustment for you, it is also a big change for her. It is only normal for her to feel anxious during this transition time. You can ease her anxiety by sticking as close to a schedule as possible, providing regular exercise and keeping the home life calm. While these may seem like small things, they go a long way in easing your pup's anxiety, which will reduce her whimpering.
Puppies sometimes whimper because they feel insecure. If you notice your pup walking around whimpering for no reason, it may be because he lacks confidence. You can build his confidence by working with him in short training sessions each day. Teach him basic obedience, such as how to walk on a leash and to sit and lay down on command, as well as tricks, such as bringing you a toy after you toss it for him. Spending time with him and teaching and praising him strengthens the bond between you both and boosts his confidence.
If your puppy is whining in the crate, either at night or when left alone, your best bet is to ignore the behavior. As long as the crate is a comfortable size and she isn't left for an unreasonable amount of time, she will soon learn to accept the crate and quit whimpering. If you respond to her whines with soothing talk or reach through the bars to scratch or pet her, you teach her that this is an acceptable way to get attention.