Its clear what the problem is, he doesn't want to be away from you! He obviously feels more comfortable with you, and doesn't understand how one day his mom and dad can both be there and then the next he has to go visit one while not being able to see the other. If you were working part time and your husband full time he spent more time with you and therefore isn't used to spending nights alone with his father, especially if he's sleeping alone. Put yourself in his shoes, and see this the way he does. A three year old can't grasp the idea of separation, and what about your husband. Did him and your son always get along? Is your son frightened of him, does he yell a lot? These are all things you have to take into consideration. The well being of your child is most important, and a child at such a young age can be so deeply affected by the smallest things, don't toy with his emotions. I know its hard to tell your husband he can't see his son, and of course he has legal rights, but if you can prove that its affecting the mental stability of the child, and isn't in the best interest of the child to be there all of the time, maybe you could change this. I don't know if this is an option but perhaps only have him sleep there one every other week, and the father can come visit him with you there the other times, it won't cause the son the anxiety of not being with his mother.
It sounds like you need some time to go through the grieving process of loosing your spouse (whether or not you wanted it) and seeing him all the time seems to make it harder for you which in turn makes it hard for your son.
Once you're not as upset over the loss, your son will be happy again. Maybe the visitation could be altered to every other weekend Friday evening - Sunday evening. Now that you work full time, you need to have that quality time during your free days off as well (equal weekend time). If that's not enough for your ex, I don't see why one evening a week day wouldn't be doable.
During your weekend alone you could join a singles activities group and find yourself again. This will speed up your grieving process and help you get over it.
Your son is telling you he wants to be with you, till he gets a bit older it may be best for him if he is with you and sees his Dad every other week, the upset behavior you are seeing will get worse , he needs you, tell his Dad that its the welfare of the child that is important... ..