Connor needs to steal the uniform of 1 of Church's men. They are kind enough to mark one that you can go at. Head for the marker that is over by the docks.
You can see the patrol on the left. They circle around the dock in a slow patrol. Your target is moving over to the right down the alley that is over there. Duck into the hay cart until the patrol is out sight after they check it.
Once the target goes into the alleyway, follow him in and take him down.