Return to Boston because it's time to take Lee down. Once you've made it to Boston, head to the Green Dragon and find out where Charles Lee has gone. Leave the Green Dragon and head for the harbor. When you get to the area marked in green, activate Eagle Vision and start walking around the docks until you find Charles marked in gold. Close in on him and he'll bolt.
There are two constraints for this part and they are not particularly easy. You need to keep Charles within 50 meters and not shove anyone while running. It may take a few tries to get it just right because there's a lot that can go wrong or slow you down here.
Chase after him and you'll see a couple of soldiers block your path. Run along the left side of the pier and let them destroy the barrel on your right (too far right and it will stun you). After that has been destroyed, go far right and use the crates that form stairs to get a little bit of height to get past these soldiers. Do the same for the next set of soldiers and then go far left for the third set. Run along the left side of the pier and jump diagonally left when you get close enough to do so.
From here, follow Charles Lee as he runs into the burning ship. Slide under the rail and then when the pieces fall, climb up the broken wood on the right. At the top, turn left and jump to the ropes which you can use to swing yourself to the platform ahead.
On this platform, more debris will fall, allowing you a low barrier to hop over to the right. Jump over that, go outside and then run along the outside of the ship until you catch up with Lee on the top deck.
After the cutscene, walk out of the ship and go straight ahead. Watch to the right for some steps that will lead you up to the pier and then walk to the end of the pier to find the Harbor Master. Talk to him to charter a ship up the river.
