Gygax and Arneson invented role-playing games and deeply influenced many CRPGs and fantasy novels. They are the great inventors.
Moving to the present, 3.0 was certainly inventive, and Jonathan Tweet (ars magica, over the edge, omega world), Skip Williams (behind the much loved/hated 2ed Options books), Monte Cook (CoC D20…), and Peter Adkinson (Wizards of the Coast) all can take some credit for being gaming innovators—though I wonder what some of them have done for us lately…
However, right now, in an admittedly very competitive RPG environment, Green Ronin seems to be my innovator of choice, and I would have to say Chris Pramas (head honcho), Scott Bennie (Testament) and Steve Kenson (Psychics Handbook, Mutants and Masterminds, Blue Rose) win the title