Most of this is general advice, since I haven't played Portugal in many, many patches.
I'm no expert but there are more money to be done in Americas than in Africa. However, going around Africa is a good way to "hop" to India (remember that you get Goa via an event) and then later Spice Islands). When you bring back the trade from Asia to Sevilla, you make a ton of cash.
So maybe "secure" India way via Africa but in the same time, go to Caribbeans or Brazil (you may avoid North America).
Most of the Americas are worthless, but this is good advice. The Caribbean's ok and you'll want it to control trade as Portugal anyways. Mexico and Peru are good places to conquer as well. Snipe the Centers of Trade and get some CN's started, but don't colonize in the Americas much other than that. You'll have to babysit your CNs a bit a first so they don't get killed by the natives or rebels.
Thank you everyone! So should I put all my new colonies under a trade company? Also, does putting a colony under a trade company make it more profitable?
There's a mapmode to show you where Trade Companies and Colonial regions are. Trade Company land (Africa/Asia) is where it's at, especially the East Indies and India. Colonize your way east. Once Goa's in colonial range, you'll get it quickly (12 months MTTH) via an event. Be careful with the Indians - if they grown large, they might want your land. If they're small and behind in tech, conquer them as soon as you can before they get big. You can then put everything into Trade Colonies and watch the ducats flow.
Trade companies are the most OP (some might say broken

) part of the game. They give you nearly all the benefits of states due to the zero autonomy, but only require territorial cores. On top of that, most of the TC land is also high development with good trade goods. You want as much if as you can get. Eventually, you'll want to control most/all of the Zanzibar and Cape trade nodes (and Aden if you can). You can collect in Zanzibar and little to no trade will leave, leaving you quite rich.
You can make some individual provinces in Africa and Asia into trade companies. They'll increase trade power and can go down to 0% autonomy but you can't change their religion and they don't contribute manpower or taxes. It's usually worthwhile.
If you build tax or manpower buildings, TCs will contribute more cash/manpower than territorial cores. Every building in a TC is 4x more effective than in a territorial core and
just as effective as in a state core. They often contribute some decent tax/manpower even without the buildings because there's usually a few additional modifiers to bring the total tax/manpower above 0%.
... (Don't forget to convert new clay before adding it to a trade company.)...
Unless you're going for One Faith, there's not much of a need to convert TCs as they don't suffer the penalties. However, if you do have quick conversion times (<10 months) and your Tolerance of the True Faith is high, go ahead and convert before assigning to a TC.