Talk to Achilles in front of the manor and you'll set off for Boston. When you get there, follow Achilles around town a little bit and then head for the General Store. You'll talk to the shop keeper and pay for the supplies before meeting back up with Achilles.
Achilles will lead you into a town square where people are protesting. He will send you to tail a man who was just talking to your father. Immediately scale one of the nearby buildings and start following this man as he makes his way through the streets. He will eventually come to a yard and climb up to the rooftops. As he climbs, be sure to get behind something so he doesn't notice you. At the top, he will make his way to a position over looking the square. When he does, come up behind him and kill him.
After you kill him, you need to escape. There's a constraint for escaping within 1 minute 15 seconds. To do this, head NE towards the waterfront and you should be able to find a building that has some birds on the corner just outside the red circle. Run up to these birds and jump off from where they were. This should do a Leap of Faith that will land you right in a pile of hay. Stay here until the red coats go away.
Another option if you can't find this spot is to jump into the water and stay close to the wall until guards come up and then dive under water until they leave.
