I did this same thing last weekend, only I wanted to drill a side overflow into my sump tank for automatic water changes. I too could not find a glass place willing to drill a glass aquarium even though I called many of them. The best they would tell me is that they would drill the glass if I could seperate it from the tank. If you've tried this you found as I did, it's asking the impossible.
I went to home depot and bought the largest glass bit they had which was (1/2") and bought a cheap 10gal tank to try it on. I did some searching on the internet for how to drill glass and found a number of links, which I'll add to the end of this.
Anyway I managed to drill the 10gal tank no problem, however, with the hole only being 1/2" in diameter I figured I'd need at least 6 to 8 of them to get an outgoing flow rate that exceeded the incomming flow rate. I abandoned this idea figuring it would be a chore to get a water tight seal on that many holes.
I found a cheap 40mm diamond coated glass drill bit on ebay, seller was
lautszyan0@netvigator.com from Hong Kong. I bought some bulkheads from Big Al's online that would fit in a 1.5" hole (close to 40mm).
I have a small cheap benchtop drill press in my garage. I mounted in on the edge of my workbench with the table over hanging. I clamped some scrap wood to the bench to support the tank, and mounted the tank on it's side with the drill press table inside the tank. I also attached a small piece of wood to the metal drill press table to protect the table and the glass that would be in contact with it.
After marking my holes with magic marker I used my daughter's play dough to form a bowl around where I was drilling to fill with water. I set the drill press to the slowest speed (500rpm).
For the drilling, it is a little different than drilling through wood. You dont drive the drill bit through the glass, you allow it to just come into contact and rub it's way though very slowly. It took me about 30 mins to grind my way though 1/8" glass and about 45 mins to grind my way through 1/4" glass.
The sites I found strongly recommend that you drill part way through on one side then flip the glass over and finish from the other side. I did not do this because the top of my drill press would not fit inside the tank. As a result when the bit came out the other side on the 40mm holes, it was not a nice clean sharp edge, but instead had some tiny minor chips around the inside corner of the hole. Not a big problem since the bulkheads I bought have a large rubber gasket that completly covers all the chips, however, I'd imagine that if the bulk heads ever experience a good strike from something that is where a crack will form.
The best tips I can give you are, start cheap, that way if you screw up your not out much, and wear hearing protection. Some of the squeeks that were produced while drilling would resonate in the tank and get loud enough to get your ears ringing. At no time durring drilling should the drill bit get hot to the touch.
As promised here are some of the links I found:
http://www.drillglass.com/drillingglass.html
http://www.uhh.hawaii.edu/~pacrc/bigisaquapg/Drilling.htm
http://www.wetdryfilter.com/drilling_holes.htm