Thanks for the additional information. You've actually got two issues going on here, so let's address them one at a time, okay?
First the crate training...
I am a big fan of crate training. Dogs are den animals. They don't demand much. They don't clamor for a giant master bedroom or a pile of feather pillows, but they do wand and need a quiet place in the house that they can all their own.
A few crate dos and don'ts should help get him adjusted to the crate:
*Make sure the crate is only big enough for your puppy to stand up and turn around in easily. If you picked a crate to match your puppy's eventual adult size, temporarily insert a divider until he gets bigger.
*Let him investigate the crate on his own. Encourage his curiosity by tossing in a toy or a few treats.
*Feed your pup in his crate. Quietly close the door while he eats and then open the door after he eats and let him go outside to go to the bathroom.
*Make the interior of the crate comfortable with a blanket or old bath towel and a chew toy to keep him occupied.
*Never put the puppy in the crate as punishment at this age. Select a different time-out location, like a bathroom, when you want to stop an unwanted behavior.
*Start with small amounts of time, and then work up to longer periods of time where he's in the crate.
Also... you need to keep in mind that your little guy is still just a tiny puppy who is getting used to all this stuff. I promise he'll grow out of the whining and learn to love his crate.
As for the house training...
Unfortunately, puppies always tend to be hard to housebreak...and when you consider the fact that your pup is really young, you have to expect there to be a bit of a challenge when housebreaking him.
Part of the issue we see with puppies is that they simply have smaller bladders than their larger counterparts and often the owners (myself included) aren't as consistent with house training as they would be with a larger dog. We worry that putting these little guys outside in the cold or wet could make them ill and we dismiss the messes in the house as minor mistakes written off to bad weather or the fact that the dog is 'just a puppy'. However, small puddles and piles add up to bigger problems that need to be addressed and all dogs..regardless of their size...need to learn the bathroom is outside.
Of course, the first thing to do is to have your vet take a quick peek at her. There are some medical problems such as urinary tract infections that can cause a dog to eliminate in the house.
If the medical exam comes back clear, then we need to start from the beginning and retrain your dog to use the bathroom outside. Establish a routine where your pup is taken outside first thing in the morning, after each playtime and before bed. Keep in mind that dogs generally need to urinate or defecate (or both!) about 20 minutes after they eat, drink or have playtime, so pay attention to the time and make sure the dog gets outside during this time frame. When he potties outside, make sure to give him lots of verbal praise and some tasty treats (I love freeze dried beef liver...available at any petstore). If you happen to catch him going in the house (and you probably will in the beginning), clap your hands loudly to startle him, then pick him up and take him outside. As soon as he goes outside, again, give lots of praise and treats. Make a VERY big deal of it so he knows you're pleased.
Keep in mind that accidents are going to happen during this training time, and no matter how frustrating it is, you need to try not to vent this frustration. When you get upset, your dog stops trying to learn and can become fearful, anxious or confused. It's also silly to discipline the dog when he eliminates in the house because all he'll do then is learn to sneak away and go to the bathroom where you're not looking to avoid getting in trouble.
Another key step is to make sure you clean the places he's eliminating with an enzyme based cleaning product, rather than something that contains ammonias or other harsh chemicals. The enzymes actually break down and destroy the protein particles in the feces/urine instead of covering up the scent. Some of these non-enzymatic cleaners actually smell enough like ammonia to bring the dog back to the scene of their crimes. You can pick up an enzyme cleaner at any Home Depot, Menards, Ect.
At this point, you should also keep him off your bed. Partly because by keeping him off the bed you'll keep him from being able to go to the bathroom on it, but also because both dogs and people tend to sleep better when they have their own space. You can have a second crate in your room for him so that he can see you and be close to you without worrying that you're going to wake up to a mess.
I know it's frustrating to get puppies house-trained...but with a great deal of consistency and patience, you can get it done!
I hope this helps.