I would guess that many claims come from the same source, i.e. the writings of Bartolomé de las Casas.
I won't read it all, but Chapter 2 describes "the first island which was found by Christians":
This page describes cutting off hands and tying them to the victims' body, telling the victim to take letters to those who had escaped into the mountains (this was to punish the Indian's first revolt, not as a punishment for not getting enough gold).
This page describes using hunting dogs.
I have linked to a French translation because I don't read Spanish. The French and Dutch were partisan/biased against the Spanish, and the original author (Bartolomé de las Casas) had a religious or political agenda in writing this account, but I have no great reason to doubt their veracity.
More importantly I think that Bartolomé de las Casas is an origin of the claims in the OP. The Oatmeal article says,
All of the information in this essay came from A People's History of the United States, by Howard Zinn, and Lies My Teacher Told Me, by James W. Loewen, both of which uses primary sources such as eyewitness accounts, journal entries, and letters from Christopher Columbus himself.
And alleged extracts from Lies my Teacher Told Me says,
All of these gruesome facts are available in primary source material- letters by Columbus and by other members of his expeditions-and in the work of Las Casas, the first great historian of the Americas, who relied on primary materials and helped preserve them. I have quoted a few primary sources in this chapter. Most textbooks make no use of primary sources. A few incorporate brief extracts that have been carefully selected or edited to reveal nothing unseemly about the Great Navigator.
Wikipedia says that the writings of Bartolomé de las Casas were part of the origin of the Black Legend; and its summary of the Scholarly analysis on that subject includes statements such as the following:
It is neither a legend, insofar as the negative opinions of Spain have genuine historical foundations, nor is it black, as the tone was never consistent nor uniform. Gray abounds, but the color of these opinions was always viewed in contrast which we have called the white legend.
and,
... proposes an overcoming of the "false choice" between two legends, to present an approach that appreciates the positive results of Spanish conquest without denying or ceasing to deplore the atrocities that were perpetrated.
Both of the above imply there is no "scholarly" doubt that "atrocities" by the Spanish did occur.
