Historically a masterpiece has been a (or the) work that demonstrates an artist is capable of utilizing their medium to its fullest extent, i.e. it has been mastered. Per ye olde Wiki:

Historically, a “masterpiece” was a work of a very high standard produced by an apprentice to obtain full membership, as a “master”, of a guild or academy in various areas of the visual arts and crafts.

In that light, I’d say the best qualified would be games that completely utilized the capabilities of the platform they were designed for or, perhaps of interest to more people, expanded what everyone thought could be done with those systems. Games which were furthermore well polished and complete, and did not have much room for improvement taking into account the constraints they had to work with at the time. (For instance: No duh we could make Mario 64 run at a higher framerate and have better textures to look nicer on hardware now. That doesn’t mean it wasn’t arguably a masterpiece of its time, on the system it was on.) This doesn’t just have to be technical stuff – It could be the way the game used storytelling, its gameplay mechanics, or anything else.