That's a tough one...I probably lean ever so slightly towards FF3(6), but Chrono is one of the best games I have ever played also. You can get FF3 for game boy advance and they fixed some of the glitches from the SNES version, and the DS version of chrono is very good also.
Lol..you are just asking to start a flame war with that kind of question :-) They are both great. My personal gut is Chrono Trigger...but that has personal family stuff tied to it...so i might be biased. FF 3 (or 6 depending on how you look at it) is top notch also...your really talking 1a and 1b here.
My suggestion - Get Chrono Trigger for the DS (includes a better script + some extra dungeons. The SNES version was ported to the Playstation and is now available as a PS1 classic but suffers from load screens where as the DS version is as crisp as the orginal.
Get Final Fantasy VI (which is the FF3 your talking about) on the Playstation in Final Fantasy Anthologies, it comes with FF5, which is a great game as well (not on CT or FF3/6 level). It too is supposedly coming to the Playstation Network soon as well...