I've found that my Comcast connection here in San Francisco fairly reliably drops for a few minutes every day at around 2-3 am. Then it comes back and works find again. I've thought about calling them about this before, but I'm not sure that I want to spend a couple hours on the phone convincing them it's a real issue.
I'm in the same boat as you where making the phone call feels like a huge hassle. But it's interesting seeing a few other people with this same problem, maybe I should call them after all.
Given the timeframe, it sounds like some sort of maintenance is scheduled around that time- during "off-peak" hours.
When I've called about it they say they can't send a tech out at night to test, so nothing has ever officially be done about it.
Sounds like more of a systematic issue though if you're seeing the same thing in SF (I'm in San Jose). But like I said, it's probably been a couple months at least since the last time I had that issue, or noticed it.