It's got to be Boomer. I'm rewatching "Water" on DVD right this minute. Boomer was programmed as a sleeper to sabotage the fleet. She blows up the water tanks, which will finish the fleet. She and Crashdown are in the raptor, and she sees "positive H2O contact" flashing on her screen. She looks distressed and distressed some more. Her cylon programming is compelling her to ignore it. She fights out the words to Crashdown--run sweep again. The positive contacts come up on her screen again, and she's able to get the words out that there's water on the planetoid. From my perpsective, that's her "final five" programming/instinct fighting with her regular cylon programming. If she'd ignored the water, the fleet would have been done.
Also, why didn't she just shoot Adama in the head at point blank range in CiC? He'd have been finished, or at least permanently incapacitated. It's got
to be Boomer. Boomer deserves some happiness when all is said and done. There's a certain symmetry to her being the last cylon that makes sense.