I think the odds of it being either of those two are fairly good.
As far as government black programs go, there are always such programs running. Some you'll hear about decades from now, others that may never be revealed. But to believe that developed nations are not doing this is naive and moronic to say the least.
For the idea of UFOs being extra terrestrials, you have to take into account what level of technological evolution such aliens are at. The odds of them being even within a few thousand years of our evolution are actually quite small, alien life would likely be much simpler than ours (microbes and such) or unimaginably more developed than us (we'd have microbial intelligence compared to them), the latter of course being the one that could possibly fly to us and study us. We'd be an interesting scientific study in the same manner that scientists today study viruses, microbes, bacteria, etc. Perhaps even an experiment of theirs, in a sorta Hitchhiker's Guide to the Galaxy sorta way. Whatever the case, it'd be in their best interest to make their presence as undetectable to us as possible. Anytime we do see them or detect them may be when their vehicles or sensors or whatever malfunction in some way.
This is of course if such advanced alien life saw us with scientific interest. If such interest were lethal, we probably wouldn't be sitting here discussing this. There wouldn't be a scout force or whatever any more than we'd send out a scout to examine a spot of mold before killing it and removing it from the kitchen fridge. They'd just wipe us out nice and quick-like. Perhaps one day this could happen due to our heavy radio transmissions, maybe interfering with their interstellar communications in some way.
The odds of both cases are probably pretty high, but who can say for sure what the odds of the latter are?