Both Native Americans and Africans suffered at the hands of European colonizers. When we consider the question of who suffered more, it's important to understand perspectives. In my answer, I'll look at a variety of perspectives and compare the impact of European colonization on both groups.
The most immediate answer as to which group suffered more would be... well, both. But if we look at the Caste System (la Sociedad de las Castas), I would argue that enslaved Africans were most negatively impacted by European colonies in the New World. When colonies were created, Europeans brought with them a social system that organized the inhabitants (both free and enslaved) based on the percentage of European blood in them, or "whiteness." At the top of the caste system were the Europeans, both Spanish/Portuguese born as well as Europeans born in the New World. Underneath those Europeans were the mixed races, with preference to mixes that had higher percentages of "whiteness." Underneath the mixes were the Native Americans and freed blacks, and at the bottom were African slaves. As far as opportunity is concerned, African slaves definitely suffered the most. While Native Americans were also denied opportunities, the higher presence of African slaves on the Eastern coast as well as in Caribbean islands would suggest that African slaves were the lowest (and therefore suffered most) socially.
Politically, I would argue that Native Americans suffered the most from European colonization of the New World. Prior to European arrival, strong empires like the Aztecs in Mexico and the Inca in the Andes Mountains of South America ran efficient, organized empires. When Europeans made contact, better weapons and smallpox transmission (due to Native Americans' lack of immunity) wiped out large percentages of the populations, allowing Europeans to settle and ultimately colonize. While it's true that both Native Americans AND Africans did not have a say in colonial government (captaincies for Portuguese territories, viceroyalties for Spanish territories, and colonial governments and charters in the British colonies), I would argue that because the political foundation set by Native Americans was destroyed and replaced with European institutions, and that Native Americans were forced to suffer labor and discrimination from the new political leaders, that the Native Americans suffered more than the enslaved Africans.
For similar reasons as my political analysis, I would argue that Native Americans suffered more--because their governments and empires were replaced, and the new European colonies profited off the natural resources of Native American land, the Native Americans suffered more.
Without a doubt, I would argue that enslaved Africans suffered more at the hands of European colonial governments. While it is true that Native Americans were also forced to work (in the Andes Mountains, the old Inca mit'a system of lottery-style labor drafts was used against the indigenous populations for silver mining), a diminished population of Native Americans due to diseases like smallpox meant that a new labor force had to be brought in to the plantations of the Americas. This is where we see the intensification of slave trading from Africa to the New World. A majority of the slaves that were shipped over the Atlantic went to either Brazil or the Caribbean to work on sugarcane plantations, where conditions were notoriously brutal and life expectancy was low. As a result, more slaves were shipped in to replace the loss of labor when a slave died. This callous exchange of bodies leads me to believe that the African slaves suffered more at the hands of European colonizers, even though Native American labor was also exploited.
While both Native Americans and Africans suffered at the hands of Europeans, based on sheer brutality and physical suffering, I would argue that enslaved Africans had the harder time of living in New World colonies. While Native Americans were also forced to give up their land, lose possession of resources, and were exploited, the sheer brutality of slave trade as well as the poor treatment of African slaves puts them higher up in my analysis. To a significant extent, though, comparison is a futile exercise: the important thing is to recognize what both groups endured and carry this awareness into the future, where we hope to prevent atrocities like these.