If you go to the link, there’s original evidence of possible intentional attempts to spread smallpox to the Indians during the French and Indian War. But by British troops, not by Americans.
As far as a dispassionate account of the facts, I found a neat article.
It discusses the Ward Churchill claims of intentional genocide against the Mandan and other tribes in 1837, and blows it clear out of the water.
It turns out Congress actually had put a program in place to vaccinate Indians. Though probably inadequate, it certainly doesn’t indicate genocidal intent.
In fact, Jefferson provided vaccine for Lewis and Clark to vaccinate Indians as they traveled across the continent. Unfortunately, their vaccine spoiled and became unusable, but again it shows intent to protect the Indians against disease, not wipe them out.
Did Jefferson have vaccines to give to Lewis and Clark? Their expedition was just a few years after Jenner invented vaccination. Inoculation had been known much longer so my guess is that they were trying to inoculate the Indians. That was also effective but riskier than vaccination.