The premise of your question is not universally true--in some parts of the Americas, native slaves significantly outnumbered people kidnapped from Africa. You can often notice these places today because many of them (e.g. Mexico) still have a more indigenous and less Afro population. So obviously there isn't going to be a great answer without more specific context. Here are some general advantages to shipping slaves in from far away rather than enslaving the locals.

• Natives know the land, and are much more likely to try and escape.

• They're also likely to have some social or political connections to native people who haven't been enslaved, who might help them escape or revolt.

• They'll also probably have connections with other slaves, since they likely grew up together. That makes it more likely they'll plan a revolt.

Incidentally, these reasons apply equally well if you're an exporter of slaves rather than an importer. Larry Gonick says (and I don't recall what his source is, sorry) that the slave traders in Africa sold their most rebellious victims to the Europeans for that very reason--they can't do as much harm far away from home.

There are also a couple reasons specific to the colonization of the Americas:

• Disease: /u/DudusMcNasty mentioned malaria resistance, but this applies more generally. Africans were likely already immune to European diseases, which Natives rather infamously weren't.

• Knowledge/skills: one of the first successful export crops from the Americas was sugarcane. Africans--unlike both Europeans and Americans--had been cultivating sugarcane for centuries.

Although native Americans were enslaved it wasn't so effective as Africans. First of all, enslavement of native Americans couldn't be as far-reaching because native numbers were dwindling because of European diseases and conquest, so it never became a state-backed operation, it was mostly a colonial matter. Also, it was usually stated that some of them resisted and usually escaped, and as natives of a common area knew a common language they were more revolt-prone as contrast with African slaves who were from all over Africa and not necessarily understood each other (a reason for not teaching them Christianity in the beginning, which would involve teaching a common language) Also, it was said that an African due to physical conditions was "worth more" than the natives who were "weaker"

Source : Capitalism & Slavery by Eric Williams

No one has mentioned complicity as a factor. Slaves from Africa were captured and sold by Africans to the traders - did native Americans keep slaves too, did they trade them? I imagine if in native American society there were a stronger feeling of prohibition to slavery as a concept that it would make it far harder for traders?

This post has some valuable information on the subject of your question. I recommend the comment by /u/anthropology_nerd.

You might like to check out previous answers to were Native Americans ever used as slaves and another on the scale of the Native American slave trade in the U.S. Southeast for more information.

For anyone who is interested, /u/anthropology_nerd did a series on r/badhistory where they talk about the Myths of Conquest, and in it specifically about Aboriginal slavery and the devastating impact it often had on Aboriginal populations, including in the American South. It's called Myths of Conquest and provides an interesting read for those interested in the topic. Here is the specific entry where they talk about how slavery was often one particular way through which disease spread among Aboriginal populations.

"A Short Account of the Destruction of the Indies" by Bartolome de las Casas has a lot of insight into this. He was a member of a conquistador's party during the early decades of Conquest in the Caribbean and South American coast. It's a very interesting read but I should warn you that it's got VERY graphic descriptions of the genocide, torture, and enslavement of the native people's. He profited much from his involvement but was so affected by the horrors he participated in that he became a monk and spent a large part of his life advocating to the Pope and the King of Spain to put an end to the harsh treatment of the Americans. Part of his reasoning was that the natives were very docile and easily converted into good Christians, and that it would be a terrible sin to perpetrate such violence onto good people, especially once they had become Christian.

Instead, he advocated for the use of slaves from Africa who, he claimed, were larger and hardier and would make a better workforce, and without the moral weight of enslaving Christians.... his arguments were eventually successful; later in life he deeply regretted this decision because he eventually realized that Africans are indeed also human beings, and that he'd simply advocated for the exchange of one set of horrors for another.

Could someone please explain how the Yamasee War in particular affected the Native American slave trade? Also of interest, I've read the Portuguese in Brazil turned slave raiding into a sport which looked a lot like British fox hunts and that it was particularly devastating. If there are any experts on Brazilian history I'd like to know their take on this question.