That said, graphics should only count as far as their timelessness. FF7's graphics are definitely a mark against it in this day and age; whereas most sprite-based games from that same era still look fine today, like Breath of Fire 3.
Anyways, my decsion is split between Earthbound, Suikoden 2, and SMT Nocturne. Hands down those are the best RPG's I've ever had the pleasure of playing. The gap between them and anything else isn't even close in my mind.
I think it is interesting you consider FF7's graphics a mark against it, but still include Earthbound in contention for near 100%. Earthbound was considered an incredibly ugly game at the time of its release, and it is still as ugly as ever even today.
Earthbound's graphics are, as Eusis points out, a result of style choice and not sloppiness or inexperience. FF7 was a graphical marvel in it's time, but at the same point it was one of the first forays into 3D graphics for a videogame. The game is rife with problems that stem mostly from a lack of experience with the technology and software, and it all comes together into a hideous mess.
For a similar situation, compare SNES-era games to Atari 2600 games, or Colecovision. Many of those games are all but unplayable to most modern gamers, and I'm NOT talking about how most of them are coddled with regenerating health and auto-saves. Even as early as the NES, most game developers had figured out how to make truly remarkable graphics that stand the test of time. It takes a lot of hatred towards the game industry to hate Super Mario Brothers' graphics, for example, and I personally still like FF1's graphical style to this day.
Earthbound's graphics may LOOK like they are bad, but they really aren't when taken in context with the rest of the game. I actually don't think I would have enjoyed Earthbound as much if it weren't for the quaint NES-style graphics. And to a further point, they can hardly be said to make the game unplayable, like many early PS1 games are.