Depends.
With the boss, definitely Explosion and Lightning. Explosion deals massive damage, and Lightning isn't bad either. Plus, even if you miss sometimes, Lightning will still get the job done.
Without the boss, though, that's an entirely different story. Fully upgraded Time Arrows combined with piercing is just plain astoundingly effective. Who needs to a'splode enemies when you can turn them into harmless prehistoric creatures? Plus, piercing helps you hit multiple enemies at once, dealing all the more dino-flavored smack-down.
Hm. "Dino-flavored smack-down."
Weird.