I have an iPhone 4S, IOS 6.0.1 and recently upgraded my original Bose SoundDock to include bluetooth. I experienced the issue with bluetooth streaming interruptions, maybe once every 4-5 mins for 0.5-1sec. It has been very well documented in this discussion. I have upgraded to IOS 6.1 but the bluetooth issue persists.
What I have found is that if I turn off WI-FI then the streaming works without interruption. Clearly this is not a fix or even an elegant workaround but it does work for me. Not sure if this has been mentioned before in the discussion as I couldn't really spare the time to read all the posts in this 26 page discussion!
I notice that some people are saying that IOS 6.1 has resolved the issue for them but it seems not fixed for everyone. To those who still experience the problem, try turning off WI-FI and see if that helps. Also if you are reporting to Apple let them know that turning off WI-FI resolves the issue. It should help the people that hopefully are still working on the problem to isolate the software problem.
I have to say I am very disappointed in Apple's support on this important issue. I feel powerless to get my point across to Apple.