You aren't going to be able to drill the crank arm with any accuracy, unless you have at least a drill press and a jig of some sort(which you will have to build), or take them to a machine shop and explain what you want to do to them. A machine shop will mount them on a milling machine to hold them in place.
The crank arm shorteners look like your best bet. You can put them on and take them off, and the cranks won't be weakend by drilling holes in them.