Edit: @ThorstenS. convinced me that this is not a feasible solution (especially within the hard-science tag). So please do not take this answer into account anymore.
Desperate times call for desperate solutions. Let's take space-time to hide our craft.
You may have seen one of these graphs, that show how a 2D black hole would look like: http://www.astrosociety.org/pubs/mercury/9802/images/embedding.gif
We assume now, that there is a device, that also allows to bend space-time, but instead of just piercing a hole in it, it creates a pocket. (The concept is similar to those of pocket universes.) This pocket is still connected to the rest of the universe, but only through a very small opening. Inside the pocket the ship rests in an area of almost no distortion of space-time.
The pocket can move (and the ship with it), and some minor interaction with the space around is possible. However, the larger the pocket opening is (to enhance interaction) the more probable is detection. In the best (most-hidden) case the opening between space and the space-time pocket is of sub-atomar scale, so that most traces, that the ship generates, will not leave the pocket.
Is this hard to create? Definitively. And the amount of energy would be enormous, if no other means are found. But is it unrealistic? I think not. Space-time does some really strange things, like creating vortexes around earth. This makes the idea at least in principle feasible.