Early game choices in Colonization can make or break your run. There are a few important things to consider when choosing where to place your first colony.

Unlike in Colonization's cousins, Civilization, there is no rush to plant your colony quickly because there is no cultural or technological tree to race through. You're not even really playing against the other European powers beyond competing with them for space, so take the time to choose the best possible space.

Prairies are most abundant in the northern and southern edges of the map, and those are best for getting high food production early on. Fishing is good, but not reliable; some water tiles are better for fish than others. High food production means lots of colonists you don't have to pay for or ship to the new world, and in this game manpower is everything. With high food production comes everything else.

The single most annoying thing about Colonization is the AI's tendency to surround your colonies with dragoons, choking out your wagon trains, pioneers, and colonists even when you're at peace. This is because all four European powers are competing for space along the eastern seaboard from which shipping to Europe is easy. If you instead travel to the western edge of the map (this will take many turns) and settle on the western coasts, competition and harassment from European cavalry, privateers, and frigates will be minimal. The difference in shipping time between the western and eastern high seas is negligible even before Magellan. Settling in the west also means you find the Incas much sooner (for their scouting gold) and, if you settle near the Aztecs, you get lots of free food. It also takes longer for the Spanish to burn down all the villages in the west because they tend to work their way east-to-west.

Your navy has four functions: moving cargo to Europe, moving people and supplies to the new world, providing transportation in the new world, and defending the aforementioned shipping interests. The fifth function, stealing foreign shipping, should be considered a bonus and not sought after as a major source of income - though during early game it will probably be your primary source of guns.

• Privateers are useful, but frigates are better.
  There's a $3,000 difference in price between them, but frigates are a much better investment. They're stronger, carry (and can capture) twice the cargo, and are a decent challenge for the men-o-war at the end of the game. On higher difficulties a man-o-war will sink a privateer every time, so once you declare independence your privateers won't be good for much except moving things quickly between ports - if they aren't slowed down by the Tory fleet. If you're into stealing cargo, once you have Benjamin Franklin you can use frigates with minimal risk of retribution, and frigates will generally perform better. If you have an all-frigate fleet you also don't have to spend liberty bells recruiting Drake.
  
  
• Your first naval purchase should be a galleon.
  Since the difference in price between a merchantman and a galleon is only $1,000 there's really not much reason not to save up for the galleon; it's faster, stronger, and carries more cargo. It can also carry treasure back to Europe so you can keep a bigger portion. Once you have the galleon you can use it to ship most, if not all, of your production early-game and your starting ship will be freed up to assist your scouts and redistribute resources and colonists. Since the galleon will speed up your income, it should be much easier to save up for a frigate afterwards than it was to save for the galleon.
  
  
• Be careful about passenger ships crossing paths.
  When a unit is a passenger aboard a ship it technically has the status of "sentry". Whenever any ship leaves a tile it will try to pick up any sentry units if both of the following are true:
  
  • The ship is not on an automatic trade route
    
  • The ship has available space
  This means that when a ship leaves a space containing another ship with passengers, it will try to abduct the passengers and take them with it. This can be a problem when giving "go" orders to ships with different destinations but which pass each other.

I've ranked the best founding fathers loosely in order of importance, for different parts of the game.

• Peter Minuit
  Without him it's impossible to use much of the land in the new world without seriously angering the natives. You need them for skills and scouting, so do everything you can to avoid taking their land before you have Minuit. I have never played a game where he wasn't available in the first or second choice.
  
  
• Benjamin Franklin
  On higher difficulties this is the single most important founding father you can get. Without him the Europeans are much more likely to go to war with you at any time, and it will always be at an inopportune moment. The cash and soldiers Europe gives you will seldom outweigh the resources you consume defending yourself, so you want to be in control of your own diplomacy as much as possible. Franklin also drastically reduces the risk of retaliation when you use frigates for stealing cargo, as any war you start will likely end quickly.
  
  
• Pocahontas
  Even when playing as France, Pocahontas makes a pronounced difference in your ability to manage the natives. If you're near the Arawaks or the Cherokee she won't do much more than slow them down a little, but with any other tribe she'll make it much easier to keep the natives quiet. Remember, you lose points and trading partners for each village you burn down.

• Thomas Jefferson
  Because he gives a flat 50% increase in liberty bell production, recruiting him will make recruiting subsequent fathers more expedient.

• Peter Stuyvesant
  I have mixed feelings about Stuyvesant. If he's picked up too early he makes the game really boring, because you suddenly don't need to care about shipping. But if you wait too long you'll end up choked and starved by boycotts unless you are okay with a 50% tax rate.
  
  
• William Brewster
  Once you have the early game essentials out of the way, Brewster makes it much easier to avoid duplicate specialists and save time educating colonists.

• George Washington
  You absolutely, definitely don't want to fight the War of Independence without him. It's likely that most of your military is grey before the start of the war, and any new reinforcements are much, much more effective with him because they'll be rapidly improved to veteran status.
  
  
• Paul Revere
  Ideally he'll never come into play, but he provides a last-ditch line of defense in case your troops all get routed. Remember, you can't re-arm your troops until it's your turn again.
  
  
• Peter Stuyvesant
  You should have him from mid-game, but if you don't then you'll need to pick him up before the war. Without him it's extremely difficult to make any money after declaring independence.

• Silver is good early on, but not a sustainable money-maker. The value of silver will decline as you export it, and it will stay declined forever. It's a great booster, especially early on, but don't rely on it as a long-term economic base.
  
  
• Don't forget you can export horses! They tend to float between $300 and $800 per cargo, and they tend to sit around unused if you're not fighting a war building more troops. Always keep 50 or 100 on-hand, but you can often safely export the extras for some free cash.
  
  
• You can't automatically ship embargoed resources, even at home. For example, if Europe is boycotting your furs then your wagon trains and ships won't unload furs at any of your own colonies. You'll have to ship those manually until the boycott is lifted. Your custom houses still work as expected - in fact this is what they're for.