Actually, that may not be the right question. I know that, in the wake of Reed's first book in 1997 and a DNA study in 1998, the Thomas Jefferson Foundation has adopted the position that Jefferson did actually father Hemings's children... but still, every now and then, I come across skeptics who claim that the DNA and hearsay evidence actually point to Jefferson's brother Randolph. I think I know what to believe, but I guess I'm curious - do the skeptics have a case?
Edit: Sorry if this has been asked before, but I couldn't find anything in the sidebar, and searching the sub didn't turn up any references either.
Have you read Gordon-Reed? If not- I would suggest that you do and decide for yourself. It is a sizable book- but a good read.
It is meticulously researched and relies heavily on written archival evidence to make its claims. In fact, I would say one of the criticisms of the book (The Hemings of Monticello) is that it relies too heavily on the archived material of Jefferson, so that he ends up dominating much of her history about the Hemings family. That said, the book is an impressive study and does a lot of contextualize the relationship between Sally and Thomas.
I am not as familiar with the arguments of the skeptics- perhaps someone else here is. Jefferson, as far as anyone knows, did not leave behind anything specific claiming to have fathered her children, but thats what we would expect considering the time/place of their encounters. So it is impossible to completely disprove a skeptic who believes that the father must have been Jefferson's brother, or someone else who worked at Monticello. Historians tend to focus on what they can prove- not disprove. You want to argue positives rather than negatives. (I can't prove Aliens fought in the Revolutionary War, but I can't disprove it either.)
I would say the archival evidence assembled by Gorden-Reed is hard to ignore and seems to establish with as much certainty as can be had that Jefferson and Sally Hemings had a very close relationship that included sexual encounters which began sometime after his wife passed away- possibly while he was in Paris with Sally and her brother- but certainly sometime right after they returned.