I am in the process of building a model of a Bantam tug
The stuffing box is completely below the waterline
Any suggestions on how the seal it from water coming in

you can use some Heat Shrink over the stuffing box tube and shaft tube, this should seal it well from water. inside and outside of hull if you can.

Waterproof grease inside the tube. When installing the shaft, there should be minimal end play. At the prop end, between the locknut and the outer bearing, there should be at least a thrust washer, preferably two washers with an "O" ring between them, all with grease applied.

does BIKERBOB mean the stuffing tube box [ not the actual tube that holds the shaft ] normally the stuffing box is fitted firstly into the hull then the stuffing tube slides into the stuffing box, this is where water can get into the hull between the 2 tubes.

The item I am concerned about is the tube that the shaft passes thru (it appears this is called the stuffing tube)

It gets various names in different parts of the world. Over here, its a shaft tube. On some old wooden boats, the prop shaft was carried in hardwood (and I mean HARD) bearings at each end of a box that was stuffed with grease. Hence, stuffing box. Grease is OK on a tug, but adds too much load in a performance boat.

years ago before surface drive was the go , all shafts were underwater and there were really no issues with water intake . you might get a few drops but nothing that will wet anything , as mentioned you should grease up the shaft plus you can also put a short length of heat shrink over the shaft tube and over the flex shaft. what i mean in this is place a length of say 1 inch piece of heat shrink over the shaft at motor end then put the flex or solid shaft in then slide the heat shrink up so half is on the brass tube and half is on the shaft then apply some heat with a soldering iron to make a seal, the shaft will still turn freely with the heat shrink over it jst make sure it has some grease or oil on it.

Fairly sure that a tug won't be using a flex shaft. Flex shafts are good for forward only, tend to have a lot of end play and also tend to unwind themselves when reverse power is applied. A boat that reverses (like a tug) needs to have things fixed so that the rigid shaft can rotate easily, but doesn't allow the prop to mash itself into the rudder when reverse is applied.

yes that is correct with the use of a flexable drive shaft on a Tug Boat. one would assume it would be a solid shaft but you never know these days what is supplied in the box. wonder what the top speed is of this tug.? in reverse i mean. lol

Thanks Crapshooter
The heatshrink is an idea I had not though of
Tug will have solid shaft not flex as mentioned elsewhere
Bikerbob