I still think that Seiken Densetsu 3 had better graphics than Chrono Trigger. At least in terms of bosses (which is what I pay most attention to). As for character sprites it's a matter of preference...I thought SD3's looked better but CT's characters were a little more interesting (frog knight, random nerdy girl VS typical gladiator, typical fighter, typical valkyrie).
I've tried to choose bosses that IMO compare well, sorry if you disagree.
Dolan

VS Grand Gaia
Dolan's lower body is cut off because he climbs up a tower and hangs off the rooftop to attack you. I believe the two are fairly comparable bosses. Dolan looks a little wussy in this comparison because I couldn't find him on the right scale to match Grand gaia.
Meanwhile here are the disembodied evil creepy bosses.
Zeal's appearance here is hurt because I couldn't find a good still of her w/ the black omen in the background. The black omen's exterior is really cool looking, though IMO not as cool as the creepy dark dimension that you fight Zable Fahr in. For references sake here's a video of the black omen fight:
www.youtube.com/watch?v=QxNzs79CIvw
All that being said, I find Zeal to look really fucking ridiculous and silly looking, especially the quirky little smile she's got going there. Not to mention she's the easiest "whole party 1 HP bosses" in RPG history since her other attacks are extremely weak and she doesn't try to disable your healing.
And SD3 has the coolest final boss(es). There's 2 other possiblities, but the best is the Dragon Emperor. He doesn't just sit in one place like most boring bosses, instead he shifts positions around the screen and breathes fire across the screen. The main disappointment IMO is that he always flies off screen and then lands somewhere else - you never see his entire body envelop the screen. The least they could have done is make a big shadow before he lands...
www.youtube.com/watch?v=OWmKzE2tDEk
Now compare that to Lavos.
www.youtube.com/watch?v=D-n9LA4F3Yo&NR=1
I've never really been sure what Square was trying to get across with Lavos. Is it that he has the DNA of all life on the planet, and looks extremely lame and stupid, therefore all life on the planet is a reflection of his lameness and stupidity?

Note. This is a bad status spell. Lavos takes a uniquely stupid, absurd pose. Chrono seems to be following suit. Is Lavos infecting the characters of Chrono Trigger with his unique brand of lameness? Perhaps Lavos has only been running from planet to planet, hiding himself in the core, because on his home planet the other Lavoses made fun of him for being so ugly. Now that he's reached earth he's trying to make humans follow his path so that he feels less sad. I've never felt more sorry for a final boss. Instead of "saving the world," our motives are misdirected towards "putting this poor, god-forsaken creature out of its misery." In the secret best ending of Chrono Trigger Lavos sheds his cocoon and becomes a beautiful butterfly.
Wait. What am I thinking? Chrono Trigger does have the best graphics!

QED. Gato gets all my silver points.