I've had both (and Mercury). They both rank at the top of my list - strong and reliable. Suzuki did better with fuel and oil; it had a gravity fed oil tank mounted on top of engine (inside cowling) which made checking/filling super easy and freed up the hatch which held the former oil tank (big plus).
Finding a good Suzuki mechanic want so easy. There were 2 in the area but neither on the water and always to busy to really care about me. But Yamaha mechanics are everywhere, on the water and off, dramatically increasing my chances of finding one who I can comfortably do business with.
The Yamaha is easier for me to decipher when I pull the cover off, but I only do light work by myself (tune up, winterize, etc).
Suzuki usually runs fantastic 6 or 7 year extended warranties, which I had the chance to use once, and they paid all the bills on a $800 fix.
As of today I lean toward the Yamaha, but its a close decision