#1. Once you’ve reached the subway train tracks with Psycho, you’ll have to clear the area of a CELL patrol with a turret deployed. You then have to jump across the broken tracks to regroup with him. Enter the next area to find a group of slaughtered CELL troops. The blackbox is on the ground beside one of the corpses.
#2. Continue along the mission and you’ll reach the trainyard with heavy CELL presence. You’ll find the second blackbox at ground level, beside a body in a room in the corner of the map. You should be able to tag it on your way to this area using the stairs from the tunnel.