I did not know how to do this earlier, so I thought I'd post it here because maybe other people don't know either.

So basically what you have to do is get to high ground. Just get on a roof by climbing up the windows, or something else. To climb, just hold down RT and press A to jump.

When you are on high ground (roof, cliff, etc.) you will want to find your target, unless you already have one (maybe your notoriety is high and you are being chased be guards, idk).

Once you have found your prey, make sure he is highlighted on your target. Now you will want to pull out your hidden blade, hook, etc.

Once you have pulled out your weapon, just hit X and Connor (or whichever character you are depending on where you are on the campaign) will perform an air assassination.

I have found that sometimes that just pressing X doesn't work, so you might have to hit A as well because you might be at too far of a distance or something. You might also have to do RT and A forward so you can get closer to your target, but you should always try to get right above and behind your target to make these happen.