Sure, your program has a main() function like any C program. The default one that comes with a new Cocoa project just calls NSApplicationMain(), but you can do other actions if you'd like.
If you want to easily access the command line information from elsewhere in your program, you can use _NSGetArgv(), _NSGetArgc(), _NSGetEnviron(), and _NSGetProgname(). They're declared in crt_externs.h:
extern char ***_NSGetArgv(void);
extern int *_NSGetArgc(void);
extern char ***_NSGetEnviron(void);
extern char **_NSGetProgname(void);
Here's a blog post about these functions, and a link to the NSApplicationMain documentation.