You will note that the Black Box locations will be marked by a symbol when you are near and the coordinates will help you find them faster. Enjoy!
Prototype 2 Yellow Zone Black Box Locations
Fairview: 144, 1111 (Find it at the left of the plus shaped area, on the grass)
Fairview: 188, 1041 (On the balcony of the gated building)
Fairview: 353, 1055 (On the top of the entrance)
Fairview: 352, 999 (Behind the building, in a corner)
Oakhurst: 234, 1346 (Near the rusty small house)
Oakhurst: 122, 1229 (On a balcony near the brick building)
Oakhurst: 464, 1145 (On the roof)
Oakhurst: 312, 1191 (At the back of the church, on a ledge on the roof)
Oakhurst: 224, 1274 (On the roof)
Linden Park: 490, 1399 (on a balcony near the rusty buildings)
Linden Park: 420, 1286 (on the roof near the glass building)
Linden Park: 74, 1460 (loading docks, top of the crane machine)
Linden Park: 157, 1464 (stadium, near the broken sign)
Prototype 2 Green Zone Black Box Locations
Salt Yard Plains: 750, 1540 (near the huge building close to the parking spaces)
Salt Yard Plains: 673, 1639 (roof of the Blackwatch factory)
Salt Yard Plains: 689, 1572 (rooftop of the factory)
Salt Yard Plains: 695, 1495 (on the roof of the hotel)
Lincoln Meadows: 876, 1156 (on the building near water tower)
Lincoln Meadows: 846, 1203 (on the roof of a building near the one with the large pillar)
Lincoln Meadows: 870, 1326 (on the roof of the green building)
Lincoln Meadows: 966, 1414 (at the back of the red brick building, in the bushes)
Lincoln Meadows: 910, 1464 (roof of the hotel)
Fulton: 653, 1358 (roof of the building near billboard)
Fulton: 666, 1220 (rooftop of the factory)
Fulton: 739, 1142 (bridge near the freeway pillar)
Fulton: 726, 1261 (on the roof of the theater)
Fulton: 720, 1417 (roof of the restaurant)
Prototype 2 Red Zone Black Box Locations
Chinatown: 417, 436 (top of a building)
Chinatown: 724, 460 (top of a building)
Chinatown: 634, 510 (top of a building)
Chinatown: 457, 535 (at the top of the glass building)
Chinatown: 730, 534 (rooftop between 2 buildings)
Midtown: 687, 326 (the roof of a building in the green area)
Midtown: 748, 216 (top of the Crytiek building)
Midtown: 456, 328 (in the ruined building)
Midtown: 448, 197 (top of a building)
Midtown: 601, 230 (top of a building)
Midtown: 564, 268 (in the ruined building)
Times Square: 417, 91 (inside the huge building, close to the top)
Times Square: 469, 93 (top of a small building, near water tower)
Times Square: 556, 123 (find it on the infected building)
Times Square: 534, 84 (balcony of the infected building)
Times Square: 628, 130 (enter the building and go down the stairs)
Times Square: 719, 67 (top of the train station)
Times Square: 679, 103 (top of the green building)
There you have it! All the Black Boxes are bow yours!