What is the best weapon for stealth kills?

The best stealth weapon is still the bow - regardless if you're using the Recurve or Compound versions; both have a base damage of 1200 which can be increased further by upgrading it multiple times. The Compound Bow however has a bit more accuracy but the Blood Dragon Recurve bow looks a lot cooler.

The elite bows can deal massive raw damage, ignoring armor while maintaining complete silence. At Rank 2, you can use the Slingshot since it can also load arrows. Once your bow reaches damage around 1920 (+12 upgrades), it will be capable of killing elite enemies with one shot and dealing 5-digit damage when hitting monstrous animals' weak points, turning it into the most powerful stealth weapon and best and hunting weapon in the game.

Other guns with suppressors have lower damage and can easily blow your cover if you weren’t able to kill the target in one shot. Guns often require headshots to kill a target instantly. This can't be done against higher-tier enemies since they were helmets; if you perform a headshot, their helmet will always break first but will keep them alive nonetheless. When using bows, you can target the body. The only downside is its range; you’ll have need to be at least medium range to ensure that the arrow hits its mark.