The Eyes of Crota is located right near the spot where the story mission The Last Array ends. It’s the furthest out from Cosmodrome’s initial spawn of the three “Crota” tasks Eris assigns you. Using the directions above for the Hand of Crota, but proceed past the darkened room, up the stairs, through the next large room where Fallen and Hive are fighting, and down a set of hallways to reach Skywatch. This is where the infamous Loot Cave was.
The building just above the Loot Cave is the Terrestrial Complex, your final destination. Keep following the linear path through the complex until you reach a large, outdoor platform. The kneeling Knight is here, and it’s in front of a glowing urn. Take out the Knight along with the rest of the Hive that spawn, then interact with the urn.