I used bottles and it was a pain, but then I never had a flood. Filling all the bottles took only about 10-15 minutes, but I also only had two racks of rats, with two bottles of water on each.

Bottles won't flood the bin.
Water lines don't run out and won't need replaced once or twice a day, and don't need rinsed out and don't make as much clackedy-clack noises.

So water system would win out on me if I went back to breeding my own rats.