Koga or Koka is less touristy and more for kids than adults.
Iga has more activities for tourist and for adults as well. Ninja costume are more elaborate than of Koga but both places are fun to visit and just an hour by train from each other.
Iga is also easier to access from the train station than Koga.
If you decide to go to Koga, you can give them a call for free pick up from the train Station.
Have Fun !