In the last scene, a bunch of human-like Cylons walk into the station where Galactica ditched the suspected Cylon. There were 9 I think. All of them were copies of the blonde and the arms dealer. Turns out the suspected guy was a Cylon after all, and the last one that walked through the door looked exactly like Boomer.
I don't think Boomer is a Cylon agent. They just made a doppelganger of her, since the real one is onboard Galactica.