You will unlock this ability in the beginning of Sequence 2. After defending the nest of Eggs from the Bobcats, you will need to use the Eagle Flight ability for the rest of the Sequence. It is possible to unlock this achievement during this short sequence, as you are required to use it in order to proceed. Follow the on-screen directions when using the ability in order to perfect your flights.
Alternatively, if the achievement does not unlock during Sequence 2, you can always use Eagle Flight during any other Sequences when traveling around Boston. This is an easier method since getting around via the rooftops with Eagle Flight is both faster and safer than roaming the streets on foot.