I do not know anything about the hydrodynamics of water
moving past/through pontoon boats.
Hopefully someone who does will chime in here.
My two cents judging by the picture you supplied:
I'd put the transducer dead center of the pontoon.
Maybe a little lower than the bottom of the pontoon.
I think you're going to get lots water turbulence coming off the
pontoon. It seems to me, the very bottom of the
pontoon will be in the deepest water, and is
less likely to aerate (add air bubbles) to the water.
Sonar doesn't shoot through air bubbles very well.
Also, don't jump the gun and figure the first place you choose is
the best. You may have to experiment, and move the transducer
several times to find the very best sweet spot.