The pilot was saying it after entering the atmosphere, it was her moment to show off, coming out of the drop, she regains control and is "in the pipe" which was the landing trajectory. Like following the line or staying inside a pipe at the correct angle and speed to the landing zone.
Thats what I always thought as a kid.
From the article Quora you pulled from another dude that looks like he should know something says:
Actually, "in the pipe," as I recall it from my Navy days (and those days were close to 50 years ago), was an aviators' term, meaning they were aimed correctly to fly on a bombing or strafing run. And as an ex-Radioman, I can say definitively that "five by five" is, as has been stated, a term meaning "reception is close to perfect." So "five by five" in the context of "Aliens" means "near to perfect," and "in the pipe" means "on target."