Stealth Takedowns are performed by perching on the wall/ceiling above an enemy, and pressing when they are glowing purple. Do this 100 times and this trophy will unlock.
You will likely unlock this easily on your Super Hero playthrough, since it is much more simple to be stealthy than it is to punch everyone, as you are much easier to kill on this difficulty. Purchasing the upgrade that allows you to Stealth Takedown two enemies at once will make this trophy much easier to obtain.
If you have completed the game and not unlocked this trophy, you can replay the Oscorp Secret Labs from the whiteboard in your apartment, which are ideal for Stealth Takedowns.