tl;dr> Patterson Brown, in particular, has argued the disunity within the Nag Hammadi Corpus. That's about the best you're going to get without defining a positive corpus, as opposed to the inverse of the canon.
The problem with answering this question is that you are asking a question akin to "Are the books not on the NY Times Best-seller list as unified as the ones that are?" At a very basic level, of course you can say that the Acts of Thecla doesn't harmonize well with the Gospel of Judas. One is popular orthodox fiction, the other is Gnostic.
To posit that every other book has some sort of cohesion is problemmatic, because "Gnostics" especially in the time of Paul and the early church, were as diverse as that heterodox entity that became the church. Furthermore, Gnostics weren't the only heterodox "false teachers" out there. Judaizers, Docetists, Marcionists, and others wrote their own books. Marcion in particular may or may not have shared Gnostics views - but his existence alone would show there is not unanimity amongst the non-canonical Scriptures.
The real question then, isn't "Do non-canonical books all agree?" but rather are there things present in the canonical ones that aren't in everything else.
There are marks of canonicity that are widely accepted, but the inverse leaves "everything else." That there should be a presumption of harmony in "everything else" is a hard thesis to make in any endeavour, let alone canonicity.
It is also useful to actually read the supposedly "suppressed" Scriptures. When you do, the differences become obvious.
To answer your question directly, then, I would invite you to check out one Gnostic "Gospel" - probably the most famous - The Gospel of Thomas. Rather than focusing on its harmony with other Gnostic Gospels (discussed below), it is probably more fruitful to understand the exact nature of its disharmony with canonical Scripture. By understanding what it does and does not purport to do, anyone should be able to see what message if any is being "Suppressed(TM)" and why.
In reading that Gospel (its short - just 115 verses), a few salient facts will jump out.
Unlike the four canonical Gospels, Thomas does not purport to give any sort of chronology. It is merely a list of the sayings of Jesus. To ask "does this line up with the account of the Gospels" is akin to asking if Gen. Custer's shopping list lines up with his battlefield report prior to Little Big Horn.
There is actually substantial overlap between the actual actual sayings that are recorded, and those found in the canonical Gospels. Rather than showing some kind of conspiracy theory that the early church tried to "Supress(TM)" these, reading it belies the Truth that there isn't anything that is "covered up." Rather, the wheat is already recorded in the Gospels, and the chaff- those parts peculiar to the Gospel do line up with what the majority of the church did accept.
John - the disciple who most stressed love ("Little Children let us love one another") - actually made the criteria explicit in canonical Scripture. (Again, it's a bit of a chicken and egg, because nobody actually said 'This is good, this isn't quite as good' until much later). He wrote in 2 John:
7 I say this because many deceivers, who do not acknowledge Jesus Christ as coming in the flesh, have gone out into the world. Any such person is the deceiver and the antichrist. 8 Watch out that you do not lose what we[a] have worked for, but that you may be rewarded fully. 9 Anyone who runs ahead and does not continue in the teaching of Christ does not have God; whoever continues in the teaching has both the Father and the Son
This would directly contradict Thomas, who records Jesus as "saying":
"If the flesh came into being because of the spirit, it is a wonder. But if the spirit (came into being) because of the body, it is a wonder of wonders.
This Gnosticism - that Jesus only appeared to flesh directly countered what the majority had "received and been taught." It wasn't evil, it was just wrong. There are "churches" that teach that "God hates fags." The overwhelming majority of Christians have rejected their writings as well. This was just an error that the majority of the church rejected. One should not be surprised if the corpus of Republican Presidential platforms is not in harmony with those of the Democrats. This is exactly why the two corpi are distinct.
The church, holding to what it had been taught and received likewise rejected this notion - and equally preserved their false writings to show it.
The traditional marks of canonicity - apostolic authorship, harmony with the received message, fidelity to the person of Jesus (again as understood by the church at the time) are simply missing in everything Gnostic or Apocraphyal. As such, these were rejected.
The result, one can show the disharmony between everything that wasn't accepted and everything that was canonical. The most famous compilation of Gnostic Scriptures - the Nag Hammadi Library is available online, and oddly enough, was perserved (once found) through the Coptic church. Other collections in the past have been available to scholars who read them. Reading them is fruitful to understand the heresies and false teachings against which the church contended in the early centuries.
But to presume everybody who disagreed with the church in exactly the same way is unreasonable. Patterson Brown, in particular, has argued the disunity within the Nag Hammadi. He posits the three most famous (Thomas, Peter, and "Truth") actually differ from the others in being closer to accepting the incarnation. He points to his proof in the linked article.
Still, the skeptic needs to define what the criteria for study is. There are differences to be sure, but finding universally accepted truths in any of the corpora is difficult indeed.