They are certainly the "best" of the gospels, but the attribution of the gospels was almost certainly after the fact. The only books of the NT that I think were properly attributed were the letters (and Revelation to the extent John of Patmos isn't considered to be John the Apostle), and even then we are pretty certain some of the ones attributed to Paul aren't his (either that or he was hit on the head and stopped writing Koine well).

I don't know where you get the assumption that Thomas is a "challenge to Christianity". Many of the sayings are similar or identical to existing ones from the NT canon. Nothing openly heretical is contained in it. If it was excluded, it was probably more because it is considered incomplete, having no narrative and just being a collection of sayings, most of which were in the four canonical gospels.

Other "Thomas" books are indeed Gnostic and/or heretical, but the Gospel of Thomas is not one of them.