Tolkien himself foresaw this confusion before the book was published in November 1954, as is revealed in a letter to Rayner Unwin (the publisher) written on 22nd January of that year: 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.

So Tolkien believed that the title The Two Towers refered to Orthanc, the abode of Saruman, and Cirith Ungol. Tolkien's letter would seem to settle the confusion but for the fact that Tolkien original cover design for The TwoTowers features a tower which is black with three horns and the sign of the white hand underneath it, which must be Orthanc (the white hand being Saruman sign). The other tower on the cover is white with a thin crescent moon above it, which is an obvious reference to Minas Morgul (Tower of Sorcery); its original name was Minas Ithil (Tower of the Moon hence the moon motif). This would suggest Orthanc and Minas Morgul were The TwoTowers.

On another level one could argue that these towers were indeed The Two Towers because both held Palanti (seeing stones) and it was through their use that much evil came to pass during the later years of the third age of Middle-earth. However, one could also argue that if the palanti determined The Two Towers then the title should be the Three Towers as three palanti were involved, the two from Orthanc and Minas Morgul and the one used by Denethor in Minas Tirith.

Another reason that throws doubt on Cirith Ungol as a contender for one of The Two Towers is in its name, Cirith Ungol - spider's pass (no reference to it being a tower). That there was a tower here is not in doubt, as Chapter 1 of Book VI is called The Tower of Cirith Ungol. What does cause doubt are the facts that Cirith Ungol was, firstly, one of many minor towers built around Mordor by the men of Numenor - others were Narchost and Carchost, fire fort and fang fort respectively or Towers of the Teeth; Durthang, dark opposition and Isenmouthe or Carach Angren, Iron Jaws. These towers / fortifications were built to stop evil from escaping from or to Mordor, but when compared to Orthanc, Minas Morgul or Minas Tirith they are not really in the same class. Secondly, The Tower of Cirith Ungol is not part of The Two Towers, it is a chapter in The Return of the King: it is sundered from The Two Towers by more than two hundred pages, which really does not help to make things clear.Whatever the arguments may be I am content to go along with the author's view, as expressed in his letter referred to above, that The Two Towers are Orthanc and the Tower of Cirith Ungol.

I recently re-read The Fellowship of the Ring only to find another oddity to the vexing subject of The Two Towers. On the very last page (in italics) Tolkien previews The Two Towers and says:- 

Orthanc
Orthanc or Mount-fang is a translation from the Elven tongue (Sindarin), which literally means forked height. It was constructed from glossy black stone, stood five hundred feet high and had been built by the Men of Gondor at the end of the second age. By the middle of the third age it had fallen into disuse and had been locked. Beren, the then steward of Gondor, gave the keys of Orthanc to Saruman in the year 2953. Hidden within the tower was a Palantir (seeing stone) which Saruman found and was thus able to communicate with Sauron who also had found one of the lost Palanti.

Minas Morgul
Minas Morgul or Tower of Sorcery had originally been called Minas Ithil or Tower of the Moon, and had been built by the men of Gondor. It was once the principal city of the southern realm and the high seat of Isildur. Minas Morgul was so renamed after it fell to the Nazg in 2002 of the third age. The tower contained a Palantir which Sauron claimed and with which he was able to pervert both Saruman and Denethor. It was completely destroyed and its foundations removed by Aragorn (King Elessar) after the War of the Ring at the end of the third age.

Information sources:

• The letters of J.R.R. Tolkien  Humphrey Carpenter & Christopher Tolkien (ed.) London: HarperCollins, 1995
• The Languages of Tolkien's Middle-earth  Ruth S. Noel. Boston: Houghton & Mifflin, 1974
• The New Tolkien Companion  J.E.A. Tyler. - 2nd ed. London: Picador, 1979
• Lord of the Rings: Fellowship of the Ring, The Two Towers, The Return of the King.
   
  J.R.R. Tolkien. - 3rd ed. London: Unwin, 1979