Are you sure it isn't just the pulsating of the el-cheapo waterpump? At least it is with ours. We have a new 2011 189FBS and the pump is very noisy and will come on every 30 seconds with no water draw. If you are getting air in the lines, it has to be at the suction end.
I bought one of these: http://tinyurl.com/2djtl7r
and installed it just after the pump--with a flexible, braided hose (with FPT fittings on both ends) between the pump and the tank. The pump is now very quiet, more like a hum, and the water flow is very smooth. I too removed the antifreeze intake stuff. I just blow my lines for winterizing, and use antifreeze in the traps only.