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