This is a complex question, and one which has both vexed and fascinated historians for decades. Much popular rhetoric about Jefferson and his contemporaries has either ignored the racial issues raised by his sweeping statements about liberty or has rather ahistorically painted him as a hypocrite. Neither view takes into account the racial assumptions held by Jefferson and his contemporaries. The egalitarian republic envisioned by Jefferson and his followers would be a white men's republic, and while Jefferson and many other Virginians held anti-slavery views throughout their lives, their racist assumptions kept them from imagining a future that included legal, political, or economic equality for blacks and whites. In Notes on the State of Virginia, Jefferson made this point explicit.
It will probably be asked, Why not retain and incorporate the blacks into the state, and thus save the expence of supplying, by importation of white settlers, the vacancies they will leave? Deep rooted prejudices entertained by the whites; ten thousand recollections, by the blacks, of the injuries they have sustained; new provocations; the real distinctions which nature has made; and many other circumstances, will divide us into parties, and produce convulsions which will probably never end but in the extermination of the one or the other race.--To these objections, which are political, may be added others, which are physical and moral.
Jefferson went on to outline the "physical and moral differences" between blacks and whites, and concluded that these differences would make it impossible for African-Americans to participate in an emerging democracy on equal terms with whites. Jefferson's first hope was for gradual emancipation combined with the settlement of former slaves in Africa. When there proved to be no political will for this, he favored the expansion of slavery into the West, which he thought would lead to the emigration of blacks from Virginia, and gradually into the West, where the institution would die out. In short, Jefferson's vision of egalitarianism did not extend to blacks, or even Indians, whose lands the yeomen farmers central to his vision of democracy would settle.
Jefferson actually specifically disparages the work of Wheatley in the same chapter, calling her work "below the dignity of criticism." As for Jefferson and Benjamin Banneker, Notes on the State of Virginia was published about ten years before his brief but famous correspondence with him.
I wonder if the above information about Jefferson's view of Africans is from a time period before or after he met people like Phillis Wheatley and Benjamin Baneker.