If I attack a strike ninja with an injection fairy lily, can my opponent activate the ninja's effect after I decide to boost damage and remove it and take no damage from the lilly? Leaving me with 2000 damage.

No they may not.

Injection Fairy Lily's effect activates in the damage step and Strike Ninja may not activate its effect during that time.

Strike Ninja can activate its effect anytime except during the damage step.

Yep..you'd have to decide to do so BEFORE the Damage Step before they boost or afterwards...assuming they use anything else.