Do you want to make, a hole for the stem and bowl? Or do you just want to just take the hole bottom off?

I don't know any other way to make a small hole in the bottom, but, taking the whole bottom off is really easy. To take the whole the bottom part of the bottle off, just take a butter knife and drop it in the bottle, so it hits the bottom hard enough and the bottom comes off in one peice. I've done this before and made myself a nice, glass hooter, that I keep in the freezer for smooth hits.

Other than that, you can try and use a normal drill bit. Just drill VERY slowly. The glass with turn bright red but eventually it will go through. Good luck.