Lee: I would suggest an 1/8" (don't think you'll find one too much smaller) paddle-type diamond coated bit designed for drilling through glass. I would secure the stones in a well padded vice or some sort of jig. Use a small spray bottle or eye dropper with some soapy water to keep the area around the drill hole pretty well lubricated. A third hand will come in "handy" (sorry!) here. It will aid in the cut and keep the bit a "bit" (sorry again!) cooler. Don't use a cutting oil or similar, it will make a mess and may stain the stones.
I would use a regular high speed drill (not hammer drill). Use a slight circular, vary the speed and do not use too much straight downward force. LET THE DRILL DO THE WORK!
You may find that when you start to break through that you'll get less chipping if you flip the rock and finish the hole from the opposite side.
I might be worth a practice run to get the feel of things.
YMMV.
Good luck!