Well, I don't believe in crate training but sometimes it is necessary. If you want him to stop, you have to ignore him. It sounds cruel and maybe it even is but it is the only way he will stop.
You have to realize you are dealing with a baby here. There are things you can do to comfort him, such as giving him a warm water bottle to snuggle, putting a clock or something that ticks in there to remind him of his mother's heartbeat. Also remember to put him out A LOT. His bladder is the size of a peanut and he just can't hold it.