Frank Zindler (The Jesus the Jews Never Knew) gives five reasons to think that Josephus said nothing at all about John the Baptist.
This is something that is not generally welcomed by those who are primarily interested in defending the possibility of any independent (non Christian) evidence at all for the historical background to the gospel narrative, but it is of interest to anyone who is interested in examining the evidence with an open mind.
Unlike the interpolation of the Jesus passage(s) into Josephus, Zindler suggests that the John the Baptist passage was inserted by a Jewish Christian or “an apologist for one of the myriad ‘heretical’ sects which are known to have existed from the earliest periods of Christian history.” (p. 96) One possibility he offers is even a pre-Christian Baptist of some sort.
Because there are details of John the Baptist in Josephus that are at odds with those we find in the Gospels many scholars, writes Zindler, have been persuaded the words about John the Baptist really were composed by Josephus. But Zindler reminds us that
many non-gospel views of the Baptist existed during the first three centuries (indeed, a decidedly non-gospel type of John the Baptist holds a very prominent place in the Mandaean religion to this day), and an unknown number of them might have held the opinion now supposed to have been that of Josephus. (p. 97)
Here are Zindler’s reasons for believing the passage in Josephus is a forgery.
The Baptist material intrudes into its context quite roughly. The paragraphs on either side of it follow perfectly if the Baptist section is removed.
I quote the paragraphs in full at the end of this post.
Paragraph  describes a king (Aretas) attacking Herod’s army and soundly thrashing it. Herod complains to the Roman emperor, Tiberius. Tiberius orders his military leader in Syria to immediately respond by attacking Aretas.
Paragraph  informs us of John the Baptist, and explains that some Jews thought that the reason for Herod’s defeat was his unjust treatment of John the Baptist. An account of John the Baptist’s teaching and practices follows. This is followed by an account of Herod arresting John sending him to a castle of Macherus where he was executed.
Paragraph  opens with the Roman military leader in Syria immediately preparing to wage war on Aretas and leaving for the heart of Aretas’s kingdom in Petra.
The passage about John the Baptist says Herod sent John to the castle of Macherus to be killed. Yet only two sentences before the Paragraph  summarized above, Josephus had written that the castle of Macherus did not belong to Herod, but to the king who soon afterwards attacked him.
Zindler notes that some argue that Macherus was really a part of the kingdom of Herod. But even if this were so, it is irrelevant to the argument. Josephus clearly believed it was part of the kingdom of Herod’s enemy-to-be. He could hardly a few sentences later have had Herod using the castle as if it were his own.
In the John the Baptist paragraph the author writes that the reason Herod’s army was defeated by Aretas was because God was punishing him for his unjust treatment of John.
But nope, that’s not the view of Josephus elsewhere. A few paragraphs later (18.7.2) Josephus writes:
And thus did God punish Herodias for her envy at her brother, and Herod also for giving ear to the vain discourses of a woman.
Josephus makes no mention of John the Baptist when discussing Herod in his other book, The Wars of the Jews.
John the Baptist is not mentioned in the early Greek table of contents to the Antiquities of Josephus, but he is found in the later Latin version.
The passages in Antiquities Book 18, chapter 5, paras 1-3
(from the Sacred Texts site)
1. . . . . So Aretas made this the first occasion of his enmity between him and Herod, who had also some quarrel with him about their limits at the country of Gamalitis. So they raised armies on both sides, and prepared for war, and sent their generals to fight instead of themselves; and when they had joined battle, all Herod’s army was destroyed by the treachery of some fugitives, who, though they were of the tetrarchy of Philip, joined with Aretas’s army.. So Herod wrote about these affairs to Tiberius, who being very angry at the attempt made by Aretas, wrote to Vitellius to make war upon him, and either to take him alive, and bring him to him in bonds, or to kill him, and send him his head. This was the charge that Tiberius gave to the president of Syria.
2. Now some of the Jews thought that the destruction of Herod’s army came from God, and that very justly, as a punishment of what he did against John, that was called the Baptist: for Herod slew him, who was a good man, and commanded the Jews to exercise virtue, both as to righteousness towards one another, and piety towards God, and so to come to baptism; for that the washing [with water] would be acceptable to him, if they made use of it, not in order to the putting away [or the remission] of some sins [only], but for the purification of the body; supposing still that the soul was thoroughly purified beforehand by righteousness. Now when [many] others came in crowds about him, for they were very greatly moved [or pleased] by hearing his words, Herod, who feared lest the great influence John had over the people might put it into his power and inclination to raise a rebellion, (for they seemed ready to do any thing he should advise,) thought it best, by putting him to death, to prevent any mischief he might cause, and not bring himself into difficulties, by sparing a man who might make him repent of it when it would be too late. Accordingly he was sent a prisoner, out of Herod’s suspicious temper, to Macherus, the castle I before mentioned, and was there put to death. Now the Jews had an opinion that the destruction of this army was sent as a punishment upon Herod, and a mark of God’s displeasure to him.
3. So Vitellius prepared to make war with Aretas, having with him two legions of armed men; he also took with him all those of light armature, and of the horsemen which belonged to them, and were drawn out of those kingdoms which were under the Romans, and made haste for Petra, and came to Ptolemais. . . .
That leaves the Gospel narratives of John the Baptist. The earliest of those describe John’s appearance and preaching as a fulfilment of prophecy. He is described as a new Elijah. The biblical authors do not attempt to explain John the Baptist as anything other than a fulfilment of prophecy, and they appeal to the passages in the Prophets, as well as the literary descriptions of the prophet Elijah, their sources of information about him.
That still leaves open the question of the John the Baptist of the Mandaean religion.