Are the Boer people of South Africa considered an indigenous people?

This is the definition presented by Douglas Sanders in his article "Indigenous peoples: Issues of definition" in the International Journal of Cultural Property: "those ethnic groups that were indigenous to a territory prior to being incorporated into a national state, and who are politically and culturally separate from the majority ethnic identity of the state that they are a part of"

Well, that is one of the several definitions presented in that article. The central premise of that article is that there is no agreed-upon definition of what "indigenous" is, and that different groups have chosen to emphasize different criteria.

In the article, Sanders does offer his own working definition as follows:

The author attempted a definition in 1995. He proposed the following: “An indigenous people is a collectivity which has descent from the earliest surviving population in the part of the State where the people traditionally lived (whether still living in that area or, as a result of involuntary relocation, in another part of the State) and which has a distinct identity associated with its history.” Indigenous minorities could be recognized in states with indigenous majorities. The definition also dealt with the problem of forced relocation, a common problem for tribes in the United States.

On that definition, Boers clearly would not count as the earliest inhabitants of South Africa.

Elsewhere, the author does mention a broader definition drawn up by Kingsbury:

To respond to arguments from India that it was problematic to try to assess which populations were the earliest in the subcontinent, Kingsbury did not want the strict historical test to be key in a definition. He suggested a “flexible” “constructivist” approach, with the following suggested elements:

Essential Requirements

—self-identification as a distinct ethnic group

—historical experience of, or contingent vulnerability to, severe disruption, dislocation or exploitation

—long connection with the region

—the wish to retain a distinct identity

Relevant Indicia

(1) Strong Indicia

—nondominance in the national (or regional) society (ordinarily required)

—close cultural affinity with a particular area of land or territories (ordinarily required)

—historical continuity (especially by descent) with prior occupants of land in the region

(2) Other Relevant Indicia

—socioeconomic and sociocultural differences from the ambient population

—distinct objective characteristics such as language, race, and material or spiritual culture

—regarded as indigenous by the ambient population or treated as such in legal and administrative arrangements.

The problems of formulating a definition are clear when one considers that the Quebecois arguably meet all the required criteria, only clearly failing on nonessential indicia.

I emphasize that last sentence because I consider it highly relevant to this discussion. Douglas Sanders points out the Quebecois as a Canadian ethnic group that are not considered "indigenous" in Canadian law, and are not comparable to Canadian first nations. That Kingsbury's definition could be used to argue that Quebecois are indigenous shows the weakness of the definition.

In the same way, Boers would seem to fit essential requirements of self identification as distinct, long connection to the region, wish to retain distinct identity, and a historical experience of disruption and dislocation.

But, on the other hand, Afrikaners/Boers have historically experienced political dominance in South Africa from the establishment of the Union of South Africa in 1910 to the end of Apartheid in 1994. In many ways, Afrikaners continue to enjoy privileged positions in South African business and society.

Also, as already stated, Boers do not represent continuity by descent from the earliest inhabitants of the regions they inhabit. Khoisan people represent descent from the earliest inhabitants of South Africa.

Finally, I'd offer one more quotation from "Indigenous peoples: Issues of Definition" that directly touches on White South Africans.

The Working Group on Indigenous Populations completed the text of a Declaration on the Rights of Indigenous Peoples in 1993. The text avoids any definition of “indigenous.”

Pressure continued from some states for a definition. India was anxious to gain support for its position that it had no “indigenous” people. An additional definitional concern developed in 1993 and 1994 when white groups from Namibia and South Africa came to the working group claiming indigenous status, leading to a protest letter signed by many indigenous delegates.

Emphasis mine.

So, when White South Africans (Sanders doesn't clarify if they were Boers) approached the UN Working Group on Indigenous Populations asserting their indigenous identity, indigenous delegates to that working group wrote a letter of protest because they did not recognize the situation of White South Africans as comparable to their own experience.

I think that Afrikaners/Boers do qualify as a distinct minority ethnicity in South Africa. However, they ultimately derive from a European settler population, and thus don't qualify as the earliest inhabitants of the land, which is often (though not always) considered an important part of the definition of "indigenous".

Also, you do point out that Boers had an experience of marginalization by British colonial government in the Cape Colony in the early 1800s, and during the Boer Wars in the late 1800s/early 1900s. However, in the 20th century Afrikaners gained powerful economic, political and social positions in South African society, enough so that they can no longer be said to be marginalized despite being an ethnic minority and the current government being led by the black majority.