IMO, FF wins the two absolute top spots, but some other Square games are better than some FF games I've played.

If I were to list all of the Square RPGs I've played, along with how I'd probably rate them on a 100 scale, then...

Final Fantasy VI (100)
Final Fantasy VII (99)
Chrono Trigger (96)
Secret of Mana (95)
Final Fantasy VIII (95)
Secret of Evermore (94)
Final Fantasy X (94)
Seiken Densetsu 3 (90)
Kingdom Hearts 2 (88)
Final Fantasy IX (88)
Super Mario RPG (85)
Kingdom Hearts (82)
Final Fantasy V (80)
Legend of Mana (75)
Chrono Cross (72)
Final Fantasy XII (70)
Final Fantasy X-2 (30)

There are a few companies that are now owned by Square that produced some excellent RPGs or RPG hybrid type games in their own time. Among these are a few I'd put in my top games I've ever played. These include Illusion of Gaia (95), Ogre Battle 64 (96), and Dragon Quest VIII (in the process of playing, so far I give it about 94).