I forget is this Boston or New York? Either way. The Liberation missions are hidden until you uncover them on the map. Eagle Points show many of them, but not all of them. You have to keep searching the still unexplored portions of the map until you come across them.
You'll definitely know when you have truly done all of the Liberation missions because the assassin you are trying to get will get a very specific mission marker on the map once done (plus you get a constant message saying go see your contact). Just keep searching the unrevealed areas and you'll come across them.
If we don't study the mistakes of the future we're doomed to repeat them for the first time.