A. "The incident was witnessed by John and me" is the correct form.
"John and I" is wrong because these words are objects of the preposition "by" and the pronoun therefore must be in the objective case (me).
"John and myself" is wrong because "myself" is correct only if the pronoun is reflexive or intensive, someone does something to himself or the word is used for emphasis:
I can take care of myself.
I will do it myself.