A "Stealth Takedown" is marked with using either of the takedown options (Web Strike or Perch) on an enemy without alerting the rest of them. This is better done in hideouts or bases, as you have plenty of places to perch and watch your enemies from above without alerting them (unless you sit directly in front of one's line of sight). There is also the Takedown option itself that appears if you walk up behind an enemy and use Square.
This is a cumulative trophy and you should be able to actually obtain this through normal progression of the story, as sometimes some of the enemies will overwhelm you if you go in webs a-blazing early in the story. If you still don't have this after completing the entire city and the storyline, return to a hideout that you've completed and start up once more webbing up unsuspecting villains.