Before starting it is worth noting that Lairs will be marked on the map by a Lair symbol to make them even easier to spot. However, all you have to do in order to set each lair as your destination is to write the following coordinates and you’re there in no time!
Prototype 2 Yellow Zone Lairs Locations
Linden Park: coordinates 407, 1344 (find it on an alleyway between two buildings). Have in mind that this Lair becomes available after you enter the Green Zone.
Prototype 2 Green Zone Lairs Locations
Lincoln Meadows: coordinates 835, 1181 (find it in a park between buildings)
Lincoln Meadows: coordinates 841, 1485 (find it in a small alleyway between two buildings)
Fulton: coordinates 702, 1278 (again a small alleyway between 2 apartments)
Fulton: coordinates 720, 1331
Prototype 2 Red Zone Lairs Locations
Midtown: coordinates 372, 217 (near the loading docks)
Midtown: coordinates 664, 225 (near the big infected building)
Times Square: coordinates 568, 130 (near an infected building)
Times Square: coordinates 661, 110 (on a street between 2 buildings, one of them in ruins)
And these are the locations and coordinates for the Prototype 2 lairs. I wish you have a great time clearing them all out!