maverickpup said:
I have been at home with him more or less 24/7 since we got him nearly 2 weeks ago..
This is actually your problem. It's really hard when you get a new puppy because you want to spend every second with them. But then they learn that you are ALWAYS around and it freaks them out when suddenly you are gone.
That doesn't mean you have to ignore him while you are home, but leave the room for a few minutes and then come back. Gradually increase the time you are away. Sooner or later he will learn that when you go away, you always come back.
It's important not to make a fuss when you leave him/come back. When I leave my boys I don't even make eye contact with them. From a person's perspective, you may think "Well wow that is mean to ignore the puppy" but in reality it makes you leaving/coming easier on them. If you are like "Bye puppy!! I'll be back soon!" they get all riled up and then suddenly you are gone. Also, not making a fuss enforces that YOU are the boss and that you have the right to come and go as you please.
The crying will get better. Don't take him out of his area when he is crying, or else that will make the behavior worse (he will learn every time he cries you will come to him, so why would he stop?

)
We crate our boys and it took Tyson about a month before he was comfortable in his crate.