She is the Queen of the Black Slime Scuttlers, and doesn't scan as Scuttler Queen. However, the game brings her up, and warns of her.
In the Slime Labs, after liberating Egon from a large containment tank, head back up the stairs. At the top, go left walk down the hall on the left. Neutralize any Black Slime along the way. The hall should take you to a small room inhabited by the Scuttler Queen. When she's surrounded by Black Slime, the Queen is impervious to attacks.
While the other Ghostbusters take on the Black Slime Scuttlers, use Slime Mines on the Black Slime in the room. Once the Black Slime is gone, disperse the Queen's P.K.E. with the Blast Stream and occasionally shoot a Boson Dart. Be sure to watch out for her projectiles and spawn. You may have to back up into the hallway to regain health.
Dispersing the Queen also gets rid of a Spirit Lock on one of the doors in the room Peter was held in. Leave the Queen's room through the door that was behind her then go left and enter the door on the left in the next room to continue the level.