Beckwith states: Because the list of canonical books is itself not found in Scripture—as one can find the Ten Commandments or the names of Christ’s Apostles—any such list, whether Protestant or Catholic, would be an item of extra-Biblical theological knowledge. (link)
But by the very arguments by which the Scriptures are Divine, they are also [proved to be] Canonical, from the method and end of their composition, as containing the rule of our faith, charity, hope, and of the whole of our living. For they are given for doctrine, for reproof, for instruction, for correction, and for consolation; that is, that they may be the rule of truth and falsehood to our understanding, of good and evil to our affections, either to do and to omit, or to have and to want. (Deut. xxvii, 26; Psalm cxix, 105,106; Rom. x, 8, 17; Matt. xxii, 37-40; 2 Tim. iii, 16; Rom. xv, 4.)
For as they are Divine because given by God, not because they are “received from men;” so they are canonical, and are so called in an active sense, because they prescribe a Canon or rule, and not passively, because they are reckoned for a Canon, or because they are taken into the Canon. So far indeed is the Church from rendering them authentic or canonical, that no assemblage or congregation of men can come under the name of a Church, unless they account the Scriptures authentic and canonical with regard to the sum or substance of the Law and Gospel.
Beckwith’s challenge should be broken down into two parts: 1) where does the canon come from, and 2) how do we know what the canon is? Each specific book declares itself to be God’s word, so God made the canon that we are required to hold to. We know a book to be God’s word by its self-assertion of authority, moral excellence, theological excellence, internal consistency and acceptance by God’s people. As soon as we know a book to be God’s word, we know it to be canonical. So our canon of scripture is derived from scripture alone.
Beckwith’s arguments are self-defeating. If we cannot recognize God’s word, then we cannot have a canon; it doesn’t matter if the word is supposedly written or spoken via the Pope. Since the books themselves tell us they are God’s word, they were God’s word and a canon before Trent. Further, the church didn’t have to wait around for over a thousand years for the pope to tell them they are God’s word.