In the above-mentioned letter, Tolkien specifically states concern about the confusion of the title — right before pouring gasoline on the fire. How? By creating his own cover art for the book. The image wasn’t used until later editions, but Tolkien’s original 1954 cover art clearly depicts Orthanc and Minas Morgul – the tower that the Nazgûl use as their headquarters. It’s the one that launches that giant glowing green beacon in Peter Jackson’s adaptation. It is close to but distinctly separate from Cirith Ungol, which is the tower nestled next to Shelob’s lair.
It is possible to deduce an answer from here, though. There are three major towers that hold the important seeing stones called the Palantiri. These structures are naturally the top contenders for titular recognition. One of these is Minas Tirith, but it isn’t really in “The Two Towers.” The other two citadels known to house the precious Palantiri are Orthanc and Minas Morgul.
The other knock against Cirith Ungol is that, like Minas Tirith, it’s a tower that doesn’t really enter the story until “The Return of the King,” when Sam enters and rescues Frodo. Cirith Ungol is also impressive, but really, it’s just one of several towers scattered around Mordor. In essence, it’s a second-tier tower that doesn’t fully factor into “The Two Towers” story.