1. Leave the dog on shore............of course I say that because my wife always wants to take the flat coat retriver, 75#.  The last trip he ended up with the least experienced paddler on the SOT. They both swam a lot. The dog gets up at the least opportune time.  I also say that because every time the dog goes in wife goes in and all of a sudden I have two or three to rescue. Also we paddle in gator waters. They don't bother people or kayaks but dogs swimming are dooable targets. A dog on the foredeck is cute but add a wave, bird, fish, snake etc and you may have a dog in the water. 

2. Look at a canoe instead..........a light weight canoe paddled by a good paddler can give the sea kayaks a run for the money. We have a fellow in the canoe and kayak club that paddles 15-16 ft canoe. He paddles it with a custom made 9ft double.......... kayak paddle, very long.   He's usually in the front unless he's doing sweep.

   I would second the light weight smaller canoe. He can get as far forward as he wants.  With a double blade paddle it is amazing how much better they go.  When we decide to take 2 dogs we take a canoe and 2 kayak paddles. Works great.

I have put a moderate size dog in the back hatch but would not do that except in calm water with a float bag.  

   Something that would work and is practical although it is not pretty is to go to Bed, Bath, and Beyond and get a bath mat with little suction cups on the bottom and attach a shallow basket the right size for your dog using string or rope.