You'd probably notice a spacecraft at a near-Moon orbit against the dark background. If you want it to hide it, the Moon surface would have been a better idea... Until we launched LRO that is. Now that doesn't quite work either.
That leaves you with the only option of leaving it in plain sight – some of the near-Earth asteroids to be more specific. If the aliens are inventive enough, they can make sure that the energy it generates, gathers and releases won't make it stand out in comparison to other asteroids. Then make it transmit, say, neutrinos amplified and shifted to regular radio waves by the relay station on Pluto. Untraceable spy satellite.