if you're gonna boil your peices you need to put them in the water while it reaches boiling, quick changes in tempature with glass is what increases risks of cracking.... and you definately shouldn't have thrown cold water on boiling hot glass.... you're lucky... i've worked with a propane torch and glass bottles trying to make a bong and i've had some pretty bad burns from the cooling (eventually i started getting far away from it while it cooled.... it's kinda hit or miss, most of the time it'll crack no matter what you do, sometimes it won't tho....) anyways, you're lucky it was only a stems worth of glass...

keep that in mind next time you're gonna boil your peice tho... put it in the water before you heat it up, and don't put even room tempature water on it (to rinse it) until the peice is at roughly the same tempature....