I think as has been mentioned that 2mm shafts in 4mm tubes are about as small as you are going to get. Beyond that you are going to have to make them yourself.
Having said that probably the only difficult part would be making a couple of bushes for either end of the tube, which should be fairly straightforward for most modellers. I would use rubber tube as a coupling, brass rod for the shaft and brass tube for the tube, all of which is easily obtainable. For the propeller you can try cutting the basic shape out of an aluminium or tin can and then twisting the blades manually when you are happy with the shape. You would then need to come up with a means of securing it to the shaft.
Another thing to consider though is that when you start getting into the realms of models that small they tend to bounce around very unrealistically on the slightest ripple and can look dissapointingly toy like. At least if you stay with a model of a couple of foot long it can still remain fairly stable on the water.
As regards rudders, when I converted a Revell 1/72nd U-Boat to surface running RC I used the kit rudders and was surprised at how manoeuvrable it is on the water.