Only document those which you're explicitly throwing yourself or are passing through from another method. The remnant is to be accounted as bugs which are to be fixed by good unit testing and writing solid code.
In this particular case, I'd account ArrayIndexOutOfBoundsException as a bug in your code and I'd fix the code accordingly that it never throws it. I.e. add a check if the array index is in range and handle accordingly by either throwing an exception -which you document- or taking an alternative path.
