This is a fun yet neglected part of the Sid Meyer game catalog. There are lots of variations mentioned above that are fun to pursue, like concentrating on building a navy. But if you are focused on maximizing your victory points, I have found only one path to do so. If I can't achieve these steps, I know I'm not going to get a entry in my hall of fame.
1. You need to have one of the earliest scouts out collecting treasure. Don't worry about converting that treasure to cash immediately, but if your AI competition gets to the great majority of native villages before you, you are not going to do well. You need this head start to win big.
2. If you have at least five or six big treasure wagons, you want to get them back to Europe before the taxes go too high. That means buying an expensive galleon. The king doesn't allow you to save much money over time without demanding payments, which makes acquiring a galleon difficult. The best way to get that money all at once is through a silver mine. Two cargoes of silver ore early in the game should get you your galleon. Save up the silver until you can do that all at once. If you can't find silver for a mine, try collecting enough manufactured goods to get that galleon price in one shot. Look for a super food city as well-- usually with multiple fish/crab resources. This may well end up being your stable/ranch city. A silver city and a food city are a great start. If you can't find silver, find a resource (sugar, tobacco, cotton) and try to get manufacturing going (rum, cigars, cloth) in that resource to replace the silver income.
3. Use your new galleon to get all your treasure wagons back to Europe, and use all that money to bring back cannon, horses, and guns for an attack on your weakest colonial neighbor. Those cities will inevitably be better than what you could build, especially at the higher levels. Instead of slowly creating your own factories, magazines, and cathedrals, steal them from the AI competition. This part demands careful planning. A few important things to remember:
a. Look for a way to get your chosen opponent into a war before you attack, or take advantage of any current war they are in. You can bribe natives to attack them, or bribe your target to attack another colonial power or tribe. Get them to move their main force far away from your target settlement (and mauled) before your attack.
b. Cannon do a great job at attacking settlements, with their 100% bonus. Use your galleon to drop cannon next to a weakly defended coastal city and drop a few infantry on top of them to defend them. Use every cargo ship you can. Delivering your army by sea is the best way to surprise them.
c. The way cultural influence works, your newly conquered cities will be mostly useless in the beginning, because you won't be able to work the tiles around it. So you need a plan that allows you to take over every nearby city of your chosen opponent in one war. You'll know the moment you've taken the last city necessary, as the influence marker (the overlaid color) will shift dramatically in your favor. You can end the war then.
d. The AI tends to make four specialized cities: a factory city, a tools/guns city, a cathedral city, and a university city; in that order. They don't tend to make a horse producing city, or a silver mine city. So your founding cities will complement the ones you just conquered. As the price of silver drops, you can eventually shift your silver ore city into an iron ore city to feed your tool factory city.
e. Churn out enough money to buy (or manufacture) the military equipment necessary to go after your other AI opponents. Multiple goods factories are not very useful, just one factory will pump out enough profit to drive taxes up to the point where you need to start your independence bid. (a second tools/guns city can be useful) But the populations of these newly conquered cities will provide you with more specialists to populate your chosen factories, and the general population will boost your final victory score. Use unspecialized colonists in these newly conquered settlements to populate your schools, colleges, and universities, and the native converts to work rural tiles. Remember that factories and some other high-end buildings add 25% each to your liberty bell production. Cities with those attributes need to be stocked with statesmen, printing presses, and newspapers. Use both money and schools to create statesmen. You'll need lots of them to get your rebellion level above 50%. You'll need printing presses and newspapers in all your big cities, which means you'll also need carpenters and lumberjacks as well.
f. If you want to keep your pioneers and universities operational while in rebellion, you'll need money (to pay the "tuition"). And if you can't sell your goods in Europe, because of your declaration of independence choice, or high taxes, you'll want to sell to the remaining native tribes. They start the game with a limited amount of money that doesn't get replenished (unless you buy stuff from them) so it's a good idea to try to "reserve" that source of funding for use during your independence fight. Don't sell too much to them earlier in the game, unless your AI opponent is exploiting that resource and you can't stop them.
4. Once you have control of the main cities of an AI opponent, make peace, and redistribute your specialists to take advantage of the assets of the newly acquired cities. Start pumping manufactured goods to sell in Europe.
5. Use emancipation to create a huge army of militia. Be ready to deploy them with guns in every city, and guns and horses in your inland cities so your new troops can be quickly moved to the coast, where the royal armies will first attack.
6. Prepare for the assault of the royal army. I like to put fortified infantry both in and next to all my coastal cities, and then create a large mobile dragoon force to counterattack successful landings. That means well connected roads. Cannon are no longer that useful (unless you have to retake a settlement). Cities on islands on the east coast will be very difficult to defend, it will also be harder to defend an empire that's separated by water. (The Royal Navy will inevitably control the seas.) Make special plans to safely get dragoon forces from one to the other (ships that can move between ports without ending a turn at sea, for example).
There are lots of fun ways to play Colonization, but the above steps I found are those necessary to get you to your highest victory scores.
It doesn't make much sense in the drive to max your final score to make a huge navy or train veteran soldiers; the investment is too high. That being said, I find it fun to explore these variations, even when I realize they are not the most effective means to the hall of fame.