No, Geralt is NOT a Mary Sue. To call him one requires redefining the term. Being an enlightened mind in a world of blind bigotry does not a Mary Sue make. Geralt doesn't walk into an area and make very intelligent, capable people become blithering idiots. He's simply specifically trained and has considerable life experience. For a character to be a Mary Sue, they need two things:
1. The character is loved, respected, and admired by all the characters for no reason or worse, despite their actions. Any respect and admiration Geralt received was earned by the time of the third game and I doubt it is universal. Don't forget the second game he was locked up for regicide and had to explain what happened.
2. The character is a walking Deus Ex Machina, able to overcome any task with no effort applied. Now call me crazy, but if that was the case, then the game would be despised for being FAR too easy.
Now if you want an example of a Mary Sue character, look up Thrall in World of Warcraft. He was essentially turned into a walking god, had his allies, enemies, and borderline deities praising him and the most active things he had done was make stupid decisions that caused world war to break out and show up at the last minute to "save the world" after the players did all the hard work. THAT is an example of a Mary Sue.