SNES by a mile. I was a working man when the Genesis and SNES were in their heyday and as such, I had to own both.
On the hardware side, the SNES smashed the Genesis. Side-by-side (yes, my friends and I actually did this stuff waaaaay back then), games like Lion King and Mortal Kombat were significantly better on the SNES. They were less grainy, had a larger color palette and the sound effects of the SNES were far superior. Finally, the SNES gamepad was unmatched. If you were an early adopter of the Genesis/Mega-Drive, you had a 3-button controller. You had to buy a 6-button controller afterward.
On the software side, the SNES again smashed the Genesis. Sega made some fun games and they had a lot of arcade ports of stuff like Altered Beast and Golden Axe. But up against the SNES, Super Mario World alone set the bar for greatness. Zelda, Illusion of Gaia, Final Fantasy, ActRaiser, Super Castlevania IV, Chrono Trigger, Secret of Mana, Super Metroid, Donkey Kong Country.....possibly the best lineup of games in any single generation. Genesis RPG's were few & far between and stuff like Toejam & Earl, Comix Zone, Sonic, Golden Axe, etc. - while fun - paled in comparison to the most polished games of the generation.
Putting exclusive against exclusive showed there was no contest to begin with. Super Castlevania IV walked all over Castlevania Bloodlines. Super Mario World destroyed all Sonic games combined. Super Ghouls & Ghosts easily trounced Ghouls & Ghosts on the Genesis.
Yep. No contest. The SNES is the reigning champion.