Auguste Nicaise, (1828-1900) was a French archaeologist who, in a public lecture entitled Les Terres disparues: L’Atlantide, Théra, Krakatoa delivered in Paris in 1885, is usually cited as linking Atlantis with the explosion of Thera. However, in that same address, he clearly expressed the view that the Azores, Madeira and others are the mountain peaks of submerged Atlantis.
Nicaise, merely mentioned Thera as an example of a civilisation destroyed by a natural catastrophe. He went on to describe the effects of the eruption on Krakatoa just two years earlier.
The text of the lecture, in French, is now available on the Internet(a).