If you specifically want to use one of the two games, it really depends on what you want to focus on. Final Fantasy VI has tools more readily available for the battle side of things (spells, items, effects, monster sprites, etc) whereas Chrono Trigger is more tightly focused on level-building (maps, events, strings, etc.). Both games have tools available in other areas, but these are their strengths.
Final Fantasy VI also seems to have a lot more dedicated hackers available, which might make it easier to figure stuff out.