You'll receive this mission after installing the second Batmobile upgrade after the main story mission in the Miagini Tunnels. APCs will be patrolling the districts with weak or no tank drone presence. After taking down an APC, you have to wait until another one appears so you need to check your Mission Select screen from time to time.
Hunting them down will earn you some extra Wayne Tech upgrade points. Take note that these APCs will have escorts so you have to chase them down while evading RPG fire and firing your immobilizer rounds. Later on, these APCs can fire two RPG rounds at a time and will be driving excellently, often taking you in the sewers and back alleys making it harder for your immobilizer rounds to get a clean lock-on. You can also use your afterburners and sideswipe to crash the escorts off the road. The remaining APCs will have more escorts and will be able to lock-on two rockets at once.
To reveal the Founders' Island APCs, you should destroy the missile launcher as part of the story so you can bring the Batmobile in the district.