Shinji stares fixedly at something. Touji peers at him reproachfully.
Toji:“Hey, boss”
Shinji:“!?”
Reichu: Toji's actually saying “sensei” (or, rather, his clipped Kansai version, sense). Now, I'm not quite sure what this implies when used among buddies, but here it's been translated as both “big shot” and “chief”.
Azathoth: Not that I know a damn thing about Kansai-ben, but I always interpreted it as a comment on Shinji's stuffiness, formality - his general sense of not being "one of the guys".
Kendrix: This scene, comic-relief laden as it may be, is quite important in that it shows us that the events of the previous episode really welded the boys together, to the point that they're having silly boy's conversation like friends do. By this point, Shinji is officially part of the pack.
If that line of Touji's actually is meant to poke fun at shinji's mannerisms, note that it's done half-jokingly in a way that shows that Touji is sure he'll get its a joke, a young-male-big-mouth thing that only furtherly underline's that he "got in"