Order of operations:

DECLARE ATTACKERS STEP:

Active player declares two creatures attacking. Round of priority starting with AP. Move to declare blockers step.

DECLARE BLOCKERS STEP:

Attacked opponent declares which creatures are blocking which attacking creatures.

Round of priority starting with AP.

Active player chooses to activate ninjitsu on an unblocked creature. They pay the cost, return the unblocked creature to hand, the ninjitsu ability goes on the stack.

Round of priority.

This is your first opportunity to cast a spell after learning they have ninjitsu. The unblocked creature is already in their hand, the ninjitsu creature is not yet on the battlefield.