The major comparison point between the two albums are their tracks which were written specifically for the inmates in each respective prison. "Folsom Prison Blues" is an indisputable classic and one of the best songs in the Johnny Cash catalog. "San Quentin" is significantly less poignant and actually comes off a bit trite when compared with its counterpart.
While "San Quentin" pales in comparison with "Folsom Prison Blues" the albums from which these tunes originate are actually neck and neck. As a matter of fact, if it weren't for the difference between those two songs, the albums would be dead even. Don't forget that At San Quentin gave us "A Boy Named Sue," which is as great a song as has ever been written (Shel Silverstein of Where the Sidewalk Ends fame wrote "A Boy Named Sue." Sometimes a Jewish cartoonist can't help but write one of the greatest country songs in the history of the genre).
Anyway, the point is that the difference between the two albums is slight. If At Folsom Prison is worthy of 5 stars (and it is), At San Quentin deserves at least 4.9999999 etc.