There are many individual car rental providers out there, however CarTrawler is the one I trust and you can rely on and I recommend. They trawl over 25 top providers including Alamo, AVIS, Europcar, National and many others for best rates and pass them on to you!
Also note that cars can be picked up at Kerry Airport, which is only 15 minutes drive from town and can be dropped of in Killarney town if you wish. Or vice versa of course.