Investigation - Examining evidence and following clues to discover valuable secrets, or researching, gathering, analyzing and decoding secret information. An obvious first pick.
Slicing - Accessing secured computer systems and lockboxes to acquire valuable (and often secret) data - again, just what an agent would do.
The third one isn't as obvious, and in my opinion any one of the three remaining Mission skills would do. Diplomacy seems to be the most intuitive one, however Underworld Trading presents another mean how to obtain more-or-less secret (and rare/illegal) stuff and info, and hence does well, too. Finally, Treasure Hunting may seem the least intuitive, but its description, The art of tracking down and recovering valuable items through the investigation of various clues, is similar to Investigation, and traditionally, secret agents are the ones send to check strange phenomena or artifacts.
Btw, my Agent has Investigation, Slicing and Treasure Hunting