The argument against Josephus is that there are no copies of his work that actually date from the pre-Christian period. All of them are copies of copies of copies, most likely done in monasteries by scribes not above slipping in a little extra something. I'm not really a scholar of these things, but apparently the evidence is that the passage in question has certain characteristics that point to it being written by a different author than the rest of the book.
If you're interested, here's a website dedicated to the argument over the reliability of Josephus:
http://www.earlychristianwritings.com/josephus.html
That snippet in Josephus' writings has been debated for many years--with both sides presenting good arguments.
I wouldn't base my faith on it.