Just so I'm clear, do you leave him in the crate all the time, or are you talking about at night?  If he's in there during the day and crying, he may be trying to let you know he has to go potty.  You may be leaving him in too long.   
The only thing I can think of is to put a box or something in his crate overnight which will only allow him enough room to turn around and lay down.  Maybe then he won't potty in the crate.  But, if he's crying you may want to try taking him out (or put him on his pee pad, depending on which method you use) and see if that's why he's crying.     |