While it appears, as SpM points out, that Tolkien wasn't sure what he ment by the Two Towers, we could still form our guesses. I would say it's Isengard and Barad-dur.
If we look in
The Breaking of the Fellowship, when Frodo is upon Amon Hen, there are places mentioned. Isengard, Minas Tirith, Minas Morgul, and Barad-dur. I don't want to quote the whole thing, since it's like a page, so it will only be the parts I'm looking at. If you wish to see the whole thing, well you know where it is.
After part about the Misty Mountains, and Anduin, Isengard is mentioned...
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Westward he looked and saw the broad pastures of Rohan; and Orthanc, the pinnacle of Isengard, like a black spike.
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Then turning south again he beheld Minas Tirith. Far away it seemed, and beautiful: white walled, many-towered, proud and fair upon its mountain-seat, its battlements glittered with steel, and its turrets were bright with many banners.
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But against Minas Tirith was set another fortress, greater and more strong. Thither, eastward, unwilling his eye was drawn. It passed the ruined bridges of Osgiliath, the grinning gates of Minas Morgul, and the haunted Mountains,....
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Then at last his gaze was held: wall upon wall, battlement upon battlement, black, immeasurably strong, mountain of iron, gate of steel, tower of adamant, he saw it: Barad-dur, Fortress of Sauron.
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These are 4 of the places being discusses that could be The "Two" Towers. Seeing that it is "Two" Towers, I think that excludes Minas Tirith, since it is "many-towered." Minas Morgul is compared to Minas Tirith, as being even greater and stronger, so that excludes Minas Morgul.
Barad-dur, the "tower" of adament, and Orthanc, the "pinnacle" of Isengard. Pinnacle=Tower. That's just my argument for the story, since Tolkien wasn't sure, and has a wide range of possibilities, we won't know, this is just how I think of it.