Hmmmm..
If you don't have an electric pump on your sink, which, of course, is the easiest solution, I'd suggest you try dropping a small flexible plastic tube down the intake tube and siphoning it back out.
Start by beginning to siphon the present water out, then kink the tube to stop the flow for awhile, and add some bleach to the tank by washing it down along the siphon tube without removing the tube.
Let the bleach do it's work, then add more water and unkink the siphon tube to resume the draining. Add more water a few times before the water level bottoms out to rinse the bleach out, then let the siphon empty the tank out as much as possible.
If there's too much water that you can't get out with the siphon, you might try using the siphon tube coupled with a shop vacuum or the supply/output tube to the foot pump.
Hope this will work! I don't have a Tom Cat, so there may be some pecularities to your system I'm unaware of.
On Edit: If you refill the whole system with water for further use this season and find a slight lingering chlorine smell or taste, you can add some baking soda to the fresh water to sweeten it. Jim (Wild Blue) described this a month or so ago:
"Now, to get back on the subject again... after you've put a small amount of bleach in the water tank, run the boat around so that it mixes well. Pump it through and out of the system. If you still have that "bleachy" smell, put a bit of baking soda in the water. In warmer climates, we sanitize the tank once every couple months or so if it isn't being used regularly." - Jim / Wild Blue
Joe.