Are you sure the crate is big enough and comfortable for him? :) I am sure it is, but its worth mentioning. Do you fee he is lonely and anxious due to being separated (ie is he separated from you during the daytime at all? If so he is more likely to be used to it.) If not, and he is only separated at night, he may be genuinely anxious and sadly it can get worse rather than the dog accepting its position. But you can also train the dog to accept being alone a bit during the day using child gates etc and making it pleasant, giving stuffed Kongs to chew and gradually adding duration..... :)
It might be worth considering a DAP diffuser. This emits pheromones just like those from a bitch with young puppies and has a calming effect. To be fair, not all owners believe they work, and it has had mixed results, but i and several others have ben very pleased with them (mine helped my dog a lot with fireworks problems :) )
They cost approx. £25 from most vets and last about 4 weeks if they are continuously plugged in (which they should be).
I do hope you get it sorted out - we all need our sleep!!

Lindsay