You can harvest/rescue or a combo of both as long as you get them all.
There are a specific amount of Little Sisters per level:
Ryan Amusements 1
Pauper's Drop 2
Siren Alley 3
Dionysus Park 3
Fontaine Futuristic 3
To check how many you need/have collected press
At the bottom of the pause screen it sasys Little Sisters in this Lavel. Above this there will be circular pictures. If all the pictures are of the little sisters face then you have collected them all. If one of the pictures is of both a little sister and a big daddy then that means there is still a little sister with a big daddy.
Unlike the first game Little Sisters are now shown on the map, just look for a pictureof their face on the map, and thats where you will find one.
Make sure that you research the big daddys to max. your damage bonus.
Achievement will pop as soon as final little sister is returned/harvested through vent.