Turned out to be warped rotors. I don't have a runout gauge, and didn't have a lot of spare time, so I ran into the local dealership when they opened (I know the mechanic and parts department pretty well) and told them my problem. They said without a doubt it was the rotors and you won't always feel a pulsing in the pedal like Dan mentioned. Send me out the door with new rotors and brake pads, took them back to the shop and got them put on. No more vibration!
I think that means I've got this car running 100%, everything is working as it should now.
COTY - 2012
Tom - 03' Bonneville SSEi', 00' Sierra SLE, 1980 Goldwing GL1100 Interstate