Lots of good ideas.
His pontoon boat is too small to put a heavy kayak on and off while on the water. Plus getting in and out of the kayak in the water could be tricky. The rope will not be pulling on the handle it will be pulling on me. Running it through the handle only guides the kayak, keeping it nose forward. If I'm not in the kayak I can't fine tune the rudder to make it track perfectly. This is not to be a high speed ride like on a tube etc, bouncing behind the boat. (no wave running)
The pontoon boat will be ran at whatever speed creates a smooth gentle water surface behind the boat, could be anywhere from 4 on up. I won't be towed "in a creek" only "to the creek" across open lake water.
The whole purpose is to get me to the creek so I can fish and then tow me back. Based on the distance from the creek to the ramp it will just mean my dad takes about 10 minutes longer to make the trip each way. I won't really be going much faster than normal, I just won't be wearing myself out paddling 2 miles each way before I start fishing.
I will definitely report back results good or bad.
Thanks for both the cautions and encouragements.

I have already been contemplating this idea. I want to use my Pontoon as a "mother ship". I am hoping I can get off and on the Kayak with out falling in. I plan to tow it with out anyone on it or possibly set it on the Pontoon as suggested. Good luck and most of all be careful.

That is awesome. Makes me want to get a sit-in!

It worked just fine. Kept speed 6 MPH or less. Very important to pay close attention at all times and keep the nose of the kayak headed toward the middle of the towing boat. You can't just sit back and go to sleep.
Next time I will put my frt scupper plugs in. The kayak had more water in the floor than usual.
It allowed me to fish a creek several miles away from where I normally put in and was not a real inconvenience to my dad and his fishing buddy.
It is not something i would do on a regular basis, but for special reasons it is very workable.