This specific achievement you will earn regardless of whether youharvest or rescue or a combo of both. However, if you are going for the other achievements in the game then you MUST rescue the little sisters.
In total there are 21 Little Sisters. Each area has a specific quota.
Medical Pavillion - 2
Neptune's Bounty - 3
Arcadia - 2
Farmer's Market - 1
Fort Frolic - 3
Hephaestus - 3
Olympus Heights - 2
Apollo Square - 2
Point Prometheus - 3
Press the Pause button and underneath Directors Commentary it says Little Sisters in this Level. If all of the pictures are of a little sister then you have collected them all in that area, if however one of the pictures shows a big daddy with a little sister then it means that one little sister is still being guarded by the big daddy.
The achievement will immediately pop when you have harvested/rescued the last girl, you don't need to wait until the end of the game.
If you are struggling taking out a big daddy I found blasting with electric shot/electric gel stuns the daddy and deals major damage, then cast target dummy and while you are reloading the big daddy doesn't bother you. This method allowed me to defeat elite bouncers on hard with no health packs.