[This post was edited on 9/3/2012 to make it more concise and more skeptical].
The booms heard near San Diego are observed by semi-expert and expert observers. Something is flying that is causing those booms.
This is less clear in Pleasant Valley and Wisconsin. Wisconsin is no where near the coast, so if the booms were caused by a flying vehicle then we would expect the boom to travel across country and this has not been reported that I am aware of. This means that they are not from a flying vehicle, unless there is some reason that they only go above a certain speed in the Wisconsin area, e.g. they are going into space or back from space. I think this is very unlikely on the present evidence.
So if there is a secret aircraft flying operationally, in contrast to a test aircraft of exotic technology, then the evidence for it involves sonic booms heard on the coast. There is such evidence at various times, but the evidence is not overwhelming and could be explained by occasional tests or other airplanes flying fast that for various reasons are not public.
So I am going to have to give an ambiguous answer here to the question of whether a black, presumably reconnaissance airplane is operational. The evidence supporting it is circumstantial, but not conclusive, and this evidence is, in summary:
1. They do spend money on secret programs which are not identified.
2. They do have a history of building and flying very secret reconnaissance aircraft,
3. There have been sightings of exotic, unidentified aircraft.
4. There have been reports of sonic booms in appropriate places (e.g. not Wisconsin).
5. The last time a new, fast, high flying reconnaissance aircraft was announced was 1964. Either they have moved entirely to satellites and slower drones, or there is a secret, fast craft of this type.
The evidence is suggestive but not conclusive. The evidence could be explained by programs to test various technologies combined with the use of various existing airframes for secret purposes.
My guess is that whatever it is, if it is anything at all, it will be "outed" in about 10 years or so from now, or about 20 years after it started flying operationally. If it exists, it is likely to be revealed for one of the following reasons
1. Disclosure for domestic political advantage
2. An operational mistake that reveals clear evidence of the vehicle
3. A disclosure by a former participant on their own initiative
4. An approved disclosure when it is no longer felt that keeping the device secret serves a legitimate national security purpose.