I managed to choke one and carry him away.

With the two left there is no way to choke the other without the one knocking at the door not noticing. I managed to Sleep dart them from far away, starting with the one not knocking on the door. The door knocker sees his comrade falling and draws his sword. But this isnt dangerous right?

I mean he doesent detect me (Only sees his ally fall) though the fact that he draws his sword made me paranoid now. Non-lethal is covered, but ghost isnt in danger either is it? I mean he may draw his sword. But he doesent see me.

As for not having bodies found this shouldnt count either right? He is a thug not a guard, and even ask out aloud "Are you asleep?"

The sleeping thug will count as a body found, but bodies found does not invalidate the ghost checkbox (and presumably not the achievement, but I can't prove that). If the other one really didn't see you, and his halo never went red, then you should be OK for ghost.

I threw an empty bottle from Granny Rags' balcony at the pile of canvassed boxes down the street to draw them away from the door. They get suspicious, but not alerted. Then they start wandering around and you can pick them off one at a time. It's tricky, but can be done if you're patient.

throwing objects and/or hitting your knife against metal are your friends, use them to seperate close groups of enemies if you are playing no-kill/ghost. makes life easy.