。
She tapped on the box with her index finger, tap tap.
Literal
She [topic-は] that box [object-を] index-finger [with-で] tap-tap [adverbial-と] tapped.
とんとん is a 擬音語 (sound mimetic) for light tapping or knocking — the rhythmic, soft percussion of fingertip on surface. The と after the mimetic is the adverbial と that follows mimetic words, attaching them to the verb they modify. たたく ('to hit, beat, tap') is a versatile verb covering anything from drumming to knocking on a door to clapping. で marks the instrument of the tapping (人差し指 = 'index finger'). 人差し指 literally means 'person-pointing finger' — the finger you point at people with.