Seneca has a greater number of wineries, but Canadaigua is a much cuter town with more going on than Geneva. I'd also say that Canandaigua lake or Keuka lake are prettier than Seneca. When are you coming? I'd rather swim/ boat in Canandaigua or Keuka, too as they are smaller, warmer and don't have currents. But as far as wineries go, Seneca takes the cake.
You can do both, Geneva and Canandaigua are about 25 minutes apart. Try staying in Canandaigua, visit Sonnenberg, eat lunch at Rheinblick , shopping along Main St. and visit/ eat at the NY Wine and Culinary Center (where you can take some cool classes, too - www.NYWCC.com) tour Arbor Hill in Bristol and travel down (great views) to the cute town of Naples on the south end of the lake, visit the Artizanns store, very cool store in Naples. tour some wineries in Hammondsport, Keuka Lake or from Watkins Glen up to Geneva on Seneca lake. Some of my fav wineries on that side are: Dr. Franks, Ravines, Herrmann Wiemer, Miles, Fox Run and Shaw. Enjoy!