If I can get a hit with the flint and steel and have plenty of time to wait for it's damage without being hit myself... Flint and steel.
If I want a farther range/instant damage with more accuracy... Arrows.
Generally, I prefer arrows. I have gotten a kill or two with flint and steel though, it can be really useful if used right. It's entirely possible to lead somebody through a narrow path and then it will be hard for them to sway away from the fire, which can do a devastating 4 hearts of damage, no matter the armor of the opponent.