I think you misinterpreted many of the responses as "attacking" instead of "helping". I did say in my response that I felt he was in his crate way too much but I wasn't implying that you were doing it to be cruel or mean or that you didn't care about the dog.
I agree with BLowry that there is a good chance he is crying because he is in his crate too often and it could help if he had more freedom with an xpen or gating off an area. I did read up on crate training and like others have said, the crate needs to be a good place to them where they feel safe. If he is put in there every time you leave the room, it probably feels like a jail to him.
Also, I read your post to my husband to get another perspective and he made a good point. I'm not saying this is the case.... but you said that your husband is getting frustrated with him and calls you when you leave because the puppy is going crazy and crying... just make sure that your husband is patient with him and doesn't yell at him or anything because that will just make his anxiety much worse (again, I'm not saying he does but I thought I'd mention it).
Tobie used to cry and cry when I would leave him with my hubby so my hubby started playing with him and giving him attention while I was gone and he quickly stopped the crying.
I also mentioned the training in my first response because you said that you were having a hard time bonding with him. Just teaching him basic commands (like sit, lay down) is so rewarding and helps with behavior problems all around because your puppy learns to listen to you and follow instruction. It will also show him that you are the leader and make him feel more secure therefore helping with the separation anxiety.
My puppy is 8 months old and I went through separation anxiety with him so yes I do have advice on stuff that helped me so if you want to PM me, I would be glad to share those with you

I think all of us truly want to help you so that you and your Yorkie will be happy
Sorry if I repeated anything anyone just said, I began typing this after BLowry's reply