Near the start of the mission, after you get told about the guard in the tower (then snipe him) you enter the same building he was guarding. Right as you walk in, there will be a crate with stinger missiles. Pick it up, continue forward and out the door to your left. Run forward, and turn back round to face the building you just left, and aim your stinger, the chopper will arrive, let the stinger lock on and then fire. The chopper will pop flares so you will miss the first shot. Run straight back into the building, grab another stinger then head out the door you originally came through to enter the building. Again, aim your stinger near the roof so you can lock on faster when the chopper reappears, lock on and shoot. BOOM! Job done.
Here is a video guide (not mine) In case you need it: