Jefferson was pretty flattering, for a man of his time, towards Native Americans, contradicting the popular view that they were inferior to whites in intellect and ability and praising native peoples as hard working, intelligent and physically equal to whites.
While Thomas Jefferson was an abolitionist at heart, advocated emancipation and even repatriation to Africa (despite the fact he also owned slaves), he did not appear in his writings to believe that blacks were equal. He pretty clearly refers to a "suspicion" that the African race was inferior to whites, and he showed a clear belief that blacks were mentally less capable than their white counterparts.
This was a very common stereotype held by both educated and uneducated whites of the time period. He also tellingly writes of his belief that, when repatriated to Africa, freed slaves must be "moved beyond the reach of mixture", meaning he did not think the black and white races should produce offspring. This is especially ironic, given the fact that Jefferson himself had children with one of his slaves, Sally Hemings.