If you mean clandestine *character* then the argument could be made for several characters. The one that instantly springs to mind is Mystique, or any other shapeshifter, but some psychics, especially mind controllers (like X-Men Evolution's version of Mesmero - he's significantly more powerful than normal Mesmero, which is saying something, because Mesmero took down his own team of X-Men in his day) and pheromone users (like Purple Man and Wallflower and her father) could also be considered very powerful clandestine characters, as their powers are more specced fore clandestine work.
However, if one was to look at just clandestine characters who could kill just about anyone in comics, I'd have to go with Bucky/Winter Soldier, or Natasha/Black Widow I, because while they may have more normal or regular power levels, at least for comics, they're the best for clandestine work.
If you mean what's the most powerful clandestine *power* it again would have to go back to preference, but shapeshifters still seem to take the highest spot on my list, watch the X-Men movies and see what Mystique does, after all, I mean, it may not be super useful in situations that don't involve some kind of subterfuge (unless you're one of the shapeshifters who also gains everyone's power when you change into them like Vanessa/Copycat and mental pattern), but it would make doing clandestine activities easier.
Of course, anyone able to get into small places, able to make themselves invisible or blend in, or anyone who wouldn't even have to be in the area to do something would be a very powerful clandestine character.
I hope this is what you were looking for.