How to prevent overseas colonies from becoming vassals?

In the Americas and Australia there is no way of preventing a colonial nation from forming. If for some reason you really want to retain direct control over colonized territories you can always focus on Africa.

For me, the bigger question is, why would you want to keep them yourself? Here's some things to consider:

1. I'm personally always out of quota to form new states out of provinces I conquer in Europe. If the same goes for you, those nice provinces you've colonized at a high cost will always remain at 75% local authority. This gives you -75% on tax income, -37,5% trade power and -75% on production income.
2. Once a colonial nation forms, tons of good stuff starts happening. They transfer 50% of their trade power to you, they start colonizing on their own, thus growing your colony without it costing you anything (might have to subsidize them for a bit to get them going), once they hit 10 provinces they give you an additional merchant and a +5% on your global trade power. Since the last update they will also ship armies to the European mainland to support you in wars. That's a LOT of good stuff and you only have to give them 5 provinces for it all to start happening. Five provinces which were not of great worth to you anyway.
3. Logistics are not an issue. You have full fleet and army access to your own colonial nations at all times. This means that there's no reason to want to prevent them forming on that basis either.

Point of attention: the colonial nation forms whenever you have 5 provinces fully colonized in a single colonial region. Them not being adjacent is not a factor.

According to the EU4 Wiki:

As long as the liberty desire is below 50%, the colonial nation is unable to declare independence, and foreign nations cannot support its independence. Two disloyal colonies may form an alliance with each other, enabling them to call each other into an independence war.

The wiki says:

The main influences on liberty desire are the colony's development, relations, and relative military strength. Some factors that are specifically relevant to determining the liberty desire of a colony are the tariff rate and the overlord's mercantilism.

A good way to get an idea on how to get it under control would be to read this. Good luck!

Also I'd like to add that I saw this after posting the answer so be wary.

This section may contain outdated information that is inaccurate for the current version of the game. The last version it was verified as up to date for was 1.21.

It's very straightforward to keep your colonial nations under your heel.

If you have the Common Sense DLC, the best option is to develop them. Their land is garbage for the most part, and development efficiency is so that it costs next to nothing around when they become large enough to want to be free. So throw a few hundred monarch points every now and then into developing a bunch of their provinces to 10 to build extra factories or whatever else you think would be useful. Every single time you hit the button to develop your colonial nation, they get -5% liberty desire. It stacks -- hit the button 10 times and they've -50%. And it decays very slowly.

The other main way is to get them into debt. If you're loaded with cash, and you usually are by the time liberty desire is a problem, build a bunch of level 8 forts on your colonial nations to ensure that their expenses are way more than what they can afford. And then pay off their debts from time to time using the subject interaction menu, for a cumulative -10% (?) liberty desire per loan paid off that also decays very slowly -- albeit from a different decay pool. One caveat here is that the colonial nations will delete superfluous forts when running a deficit while at peace. I haven't tested but I'd surmise they do so only when the month ticks, like for war exhaustion reduction. But presumably you're seldom if ever at peace by this point in the game.

This second method is the most useful with Mexico during the 16th century. Make Mexico pay for its own useless forts with its gold shipments. But build only enough forts that it has an oh so slightly positive income during peace time. It'll mothball them while at peace and usually delete most of its army. During your next war, it'll eventually take a loan to enable its forts, and build a new army if threatened. Take a look from time to time and pay off a loan for a sweet liberty desire reduction.

Note that while you can use both methods on the same subject, they don't stack well, because they use different decay pools. If you use both methods, the decay will basically go twice as fast.

Also note that both of the above methods apply to any subjects, including an enormous Brandenburg March that you can get to send officers to for good measure. With Economics, you can theoretically keep the whole American continent loyal with 100% tariffs as a one province minor this way.

If your capital is in a colonial region, you will never get colonial nations (I'm not actually sure about Australia, but if your capital is in South America, I know you won't get colonial nations in North or South America, and obviously you won't get colonial nations in the Old World).