I think you need to just go back to leaving him alone for a few minutes. Maybe start off with 30 seconds. Before you try this I'd suggest taking him for a long walk so he burns off some of his energy first and is ready to go to sleep. Put him in there, dont say anything, dont make eye contact, then hide from him, wait 30 seconds, come back and tell him to sit, then open the crate, praise him lots (but be calm, not high pitched noises), give him a small treat, then increase by 10 or 20 seconds. Usually you'd do it for a few minutes but if he's really anxious then you probably need to start off with very short periods on time.
This wont be done in one session, it probably will take a few weeks.
Is this when you put him to bed or when you leave the house? Have you tried leaving the radio or tv on?
You could also try a puppy obedience class, this will show him that you are boss and when you leave the house or leave him in his crate that its ok.
Good luck x