There are many ways to make money in Assassin's Creed III
If you know of more good ways, please edit this article to add.
Buy Treasure Chest Maps at your store
Make sure to open all chests you find
Do homestead quests to get more artisans
Complete Assassination Missions
Check your contracts and assign your recruits to assassinate them. Send only if success rate is high.
Steal from people
Slow, but works
If you run into armed templar caravans in the forests and main trails of the frontier maps, kill the guards and loot the wagons. You can get 750 pounds from small caravans and 1500 pounds from larger caravans
Do lots of side missions, many of them have good rewards
Find a location that has lots of Wolves and Cougars in it, they give a good return
South of Homestead and middle west in Frontier there is a location with Lots of Beavers in it which can also give you some money. When you find a spot with lots of Beavers, run around with Hidden Blade slaying the beavers. Lay some traps also to get more hunt.
Sell in general store or ship out in a convoy
Complete as many naval missions as you can to reduce risks to your ships.
Lower Tax Rate
Complete Fort Takeover mission, and the tax rate drops for every one of such missions you complete
Opening chests can give you recipes. After doing all the Homestead Missions (So that you have access to the most resources), build a ship. (Lance from Homestead is the ship builder). Access accounting book to check on materials. Go to stockpile to get any missing materials. Upgrade the Naval's Ship capacity.
Choose something to Craft. One suggestion is Saddles. Send the items you crafted out on your ship and sell them to people who want it. Make sure your boat is full with stuff to sell and destinations before you ship to convoy.
You can make up to 3 convoys, and upgrade each of their space up to 8, make sure to do that if using Convoys.