Has there ever been a reference to the Gorn and the Xindi-Reptilians somehow being related? According to one Federation map I've seen, Xindus, New Xindus and Gorn, in the Gorn Hegemony, are relatively close. Since both are reptilian species whose home worlds are not incredibly far apart, I believe this to be a valid question.
Unknown (but see below).
There simply isn't any canonical information from the shows or canon tie-in factbooks to make any sort of conclusive judgement. You might however want to note that their regions of influence aren't at all close, over 200+ light years away and that the history of the Xindi (as seen in Enterprise) would suggest that warp travel is a relatively recent development for them, perhaps a matter of a few hundred years.
Image from Star Trek: Star Charts
Having said all that, we learned in TNG: The Chase that the Milky Way galaxy was seeded with DNA from an an early humanoid race. It's certainly plausible (nay, likely) that both the Gorn and Xindi arose as a result of this seeding process.
We get a little bit more info about the background of the Gorn in the RPG Star Command II: Empires at War in which we learn that the Gorn aren't a single race (but in fact three) and that none of the three planets that these races had assumed were their ancestral homeworlds were in fact their point of origin, and nor was the world (Clagorn) that they all claimed as their new homeworld and capitol of their Confederacy.
Actually, the Gorn species is comprised of three different races, each having evolved on a separate planet. Soon after these races made contact, scientists discovered that genetically, all three were in fact the same species. In turn, it was discovered by examination of fossil records, that none of their three home worlds was the true point of origin for their species. This helped to quickly cement the three races into a solid political unit.
Given this and the fact that their race was apparently capable of warp travel hundreds of thousands of years before the present era, it's easily possible that the Gorn and the Xindi are interrelated in some fashion.
Comparative anatomy provides inconclusive evidence
The five surviving Xindi species share a characteristic cheek feature that might be analogous to the notch between the eye and nostril of the Gorn from "Arena":
The eyes of the mirror-universe Gorn in "In a Mirror, Darkly, Part II" have vertical slit pupils:
These are similar in form and colour to Xindi-Reptilian eyes.
The faceted eyes of the Gorn in "Arena" could be explained as transparent eyelids or artificial eye protection. Canon is silent on the matter.
Xindi-Reptilians have five-fingered hands that resemble human hands:
Gorn have robust three-fingered hands:
Although Xindi-Reptilians always wear gloves which could disguise three-fingered hands, their aggressive pride in their own species makes any imitation of other species' features unlikely.