Sure, there's some 'Black Legend' cases in South America, but that North American Native Americans were the victims of genocide is not controversial.
Disease killed many but so did mass-expulsion, slavery, scalping, starvation, countless massacres and 'Manifest Destiny'.
The 'Founding Fathers' were well aware at the time what they were doing, also in writing, and pretty much every source you can find in the period are equally unambiguous.
George Washington called the Native Americans “beasts of prey” and called for their total annihilation on many occasions, besides destroying what was virtually the stone-age people of the Seneca nation, and later the Iroquois Confederacy. George Washington gave the following orders to General John Sullivan in May 31, 1779:
“The immediate objectives are the total destruction and devastation of their settlements and the capture of as many prisoners of every age and sex as possible. It will be essential to ruin their crops in the ground and prevent their planting more.”
Andrew Jackson was behind several massacres on Creek Indians and the total destruction of many other Eastern tribes. President Thomas Jefferson wrote in December 29, 1813:
“This unfortunate race, whom we had been taking so much pains to save and to civilize, have by their unexpected desertion and ferocious barbarities justified extermination and now await our decision on their fate.”
Extermination of Indians was encouraged publicly, in the daily press or for example by the Governor of California in 1851. In 1867, General William Sherman said:
“We must act with vindictive earnestness against the Sioux even to their extermination: men, women and children.”
From 1848 to 1870 over 120,000 Native Americans died just in California. The examples are numerous.