Tolkien Gateway says:
Tolkien came up with the title under deadline pressure and later expressed dissatisfaction with it. In letters and one sketch he considered several possible sets of towers, including Minas Tirith and the Barad-dûr, and even the possibility of leaving the matter ambiguous. However, he eventually settled on Orthanc and Minas Morgul and wrote a note to this effect which appears at the end of most editions of The Fellowship of the Ring. He also produced a final cover illustration showing these towers, but the publisher decided not to use it in order to save money on the production costs.
Loosely, any pair from a set of five towers in the story could plausibly fit the title: Cirith Ungol, Orthanc, Minas Tirith, Barad-dur, and Minas Morgul.
Here's the quote from "Fellowship of the Ring" that the Gateway referred to:
Here ends the first part of the history of the War of the Ring.
The second part is called The Two Towers, since the events recounted in it are dominated by Orthanc, the citadel of Saruman, and the fortress of Minas Morgul that guards the secret entrance to Mordor; it tells of the deeds and perils of all the members of the now sundered
fellowship, until the coming of the Great Darkness
And the letters that the Gateway referenced - research shamelessly stolen from this forum - are:
A letter to Rayner Unwin (the publisher) from Aug 17, 1953 (Letters #140)
"The Two Towers" gets as near as possible to finding a title to cover the widely divergent Books 3 and 4; and can be left ambiguous - it might refer to Isengard and Barad-dûr, or to Minas Tirith and B; or Isengard and Cirith Ungol."
With the note which explains:
In a subsequent letter to Rayner Unwin, Tolkien is more definite that the Two Towers are 'Orthanc and the Tower of Cirith Ungol'. On the other hand, in his original design for the jacket of 'The Two Towers' the Towers are certainly Orthanc and Minas Morgul. Orthanc is shown as a black tower, three-homed (as seen in Pictures no. 27), and with the sign of the White Hand beside it; Minas Morgul is a white tower, with a thin waning moon above it, in reference to its original name. Minas Ithil, the Tower of the Rising Moon ('The Fellowship of the Ring' p. 257). Between the two towers a Nazgûl flies.
In the "subsequent letter" from Jan 22, 1954 (Letters #143) mentioned in the footnote , Tolkien wrote:
"I am not at all happy about the title 'The Two Towers'. It must if there is any real reference in it to Vol II refer to Orthanc and the Tower of Cirith Ungol. But since there is so much made of the basic opposition of the Dark Tower and Minas Tirith, that seems very misleading."