The essential internet site for Josephus scholars is PACE, the Project on Ancient Cultural Engagement, led by Professor Steve Mason. Incredibly, the Brill translation and commentary, which is very expensive in hardcover, is available FREE on the PACE site. The English translation appears parallel to the Greek text of Niese (provided by The Perseus Project) and commentary is seen by clicking on the footnote numbers. Clicking on a Greek word brings up the Perseus analysis tools.
Here is a link to one of the famous Josephus passages related to the OT canon, Contra Apionem 1.8
If you prefer to have the works of Josephus in your Logos electronic library, the Niese text is available morphologically tagged and including apparatus. The English translation of William Whiston can be linked to the Greek text to scroll simultaneously. The Brill translations and commentaries are available, but they are Brill-priced. The cheapest way to purchase them is as a part of the Flavius Josephus Collection. Logos has several individual monographs on Josephus, which you can find here.