In chapter 5: Urban Warfare there are several movie posters scattered around the level for fake movies starring various Naughty Dog employees.
The back of Drake's gun holster reads "NDI," which stands for Naughty Dog Inc.
In chapter 5, there are billboards that read: Club Raja and there's a hotel named Hotel Eldorado. Both are nods to the first game.
In chapter 2 ("Breaking and Entering"), the scattered newspapers on the ground list the level's designer, background artist, and QA tester as wanted felons
When Drake and Tenzin find a pack of dead wolves in the ice cave, a single red dog/wolf paw print is visible in the snow midst of all the blood, which is the development company's logo.