I had trouble finding the missing Laser Pistol too. I found it on top of the rocks at the center of the lowest point in Scorpion Gulch. There's a dead body on the ground near the rocks.
If you get the password from the dead BoS soldiers, you can get into the bunker by using the intercom.
I HAVE the SOLUTION!!!
You have to first get the tip that the laser is in Scorpion Gulch. Before that time it is not there.
Talk to the Brotherhood Quartermaster again after you agree to look for the pistol.
She will suggest talking to the firing range officer (has no name) about who last had the laser pistol.
He will say that Initiate Stanton was the last person to check it out but he turned it back in.
Talk to Initiate Stanton and confront him.
He will confess and tell you about Scorpion Gulch and where he lost it by a body.
ONLY THEN does it show up.
Spent hours looking for it