Many players ask "What is the best way to make money?".
The best source of money added to the game is elite pillages. These are ways to generate relatively large amounts of money.
On doubloon oceans, a secondary way to get money added to the game is to do massive foraging runs. This involves large numbers of labor alts, and a large amount of time. Some people feel that this is too boring; others feel that it is worth the time
One of the worst ways to generate new money is by using the navy. While this does not provide much money, it does let you practice the puzzles. In general, being good at a puzzle is one of the best ways to get invited to elite pillages.
Besides generating new money into the game, the next best way to make money is to take it from other players. This can be done by running a successful shop, winning wagers in Swordfight, Rumble, or parlor games, or providing labor to shops so they can produce finished goods. Note that none of these is a guaranteed win; while high end players of these games can generate more money than any other source of income, this is based on other players having money to spend or wager. And, be careful -- there's always someone better.
The bottom line: The best recommendation is to practice on the navy until you can do well in one puzzle (consistently doing "good" or better), then pillage with other players by taking jobs from the notice board, and finding and joining a good crew. Get to be known by your crewmates, and the people that you job around with. Talk to people, and get hearties. Be known for being good, and you will be invited to high-end pillages with other good players.