Basically the go-to historian for this is Harvard's Annette Gordon-Reed, who created a revolution in the scholarly consensus in the 90s with her book Thomas Jefferson and Sally Hemings: An American Controversy. In that book she presented several arguments in favor of the liaison having occurred which were unfairly ignored by earlier generations of historians.

The most important piece of evidence is that Thomas Jefferson was the only male in the Jefferson family who was around Monticello 9 months before Sally Hemings gave birth to each of her children. The DNA tests on Hemings descendants showed that their ancestor was a member of the Jefferson family, so many proposed Randolph Jefferson, Thomas' brother, as the father. But Gordon-Reed's work showed that the time frame only worked if Thomas Jefferson was the father.

In addition Gordon-Reed cast light on other fallacies: Randolph Jefferson was most friendly with the field slaves, while Sally Hemings was a house worker and would thus have been much closer to Thomas than to Randolph. Also there was a consistent oral tradition among the Hemings family descendants that Thomas Jefferson was their ancestor, which goes back to the memoirs of Madison Hemings, Sally Hemings' son who wrote of his parentage in a newspaper interview after Thomas Jefferson's death. Of course oral traditions are not always accurate but Gordon-Reed cast them in the context of the DNA revelations and other circumstantial evidence to make a very good case for Jefferson having been their authentic ancestor.

Of course, we can't have complete certainty but I've seen it estimated that it is 97% likely Hemings' children were fathered by Thomas Jefferson.

As for the question of whether it is rape or consensual, again Gordon-Reed's evidence seems to indicate pretty clearly that the relationship was consensual by most standards. The oral tradition of the Hemings family held that Thomas and Sally were in love, which is an odd tradition for folks to have if their family were a result of rape. In addition Sally Hemings' brothers and other family members continued to be friendly with Thomas Jefferson even after they were manumitted, and regularly visited him at Monticello, which is an odd thing to do if he was raping their sister. Likewise, Madison Hemings, in his memoirs, recalled Jefferson in positive terms as a kind man and as his father, which again would be odd if his mother had been raped.

So, I'd say to your question that there is good evidence to show that Thomas Jefferson and Sally Hemings had a sexual affair but none to suggest that their relationship was rape.

Further reading:

Thomas Jefferson and Sally Hemings: An American Controversy and The Hemingses of Monticello, both by Annette Gordon-Reed, who is probably the leading expert on Jefferson-Hemings today.