Crate training is the best. When you have to crate him put a t-shirt that you have worn in with him, maybe a t-shirt you no longer care to wear anymore that can be his. Even when you are there have something of yours that has your scent on it that he can have in his crate or even laying outside the crate. This should stop the whining.
When I crate trained Kobe, I made a divider for the already small crate so he could only lay sit and stand up. As he grew the divider was removed. He never peed. When I returned home and let him outside to use the bathroom, if he didnt use the bathroom, I would put him back in for a little longer, until he used the bathroom. He was having issues of going outside doing nothing then coming right in and peeing.
So it did not take him long to understand he best pee when taken out of the crate to the outdoors in order to have mommy time. He was trained in 4 weeks by age 4 months, and I then at 5 months I added bell training and now he hits the bell to let me know he is at the door. He is almost 6 months and I still crate him at night and when gone. He never has cried being in his crate. His crate is in the main room which I have a open floor plan so that helps since he can see me in the kitchen, at the breakfast table, dining table, sitting on the couch and even the door entrance of my bedroom.
If you plan to have him neutered, if he has a blankie sleep with that a few nights and take it with him to have in the crate before and after his surgery. This will help relax him smelling your scent and not be afraid.
Good Luck