I too have never seen Koufax or Gibson pitch so I really can't speak for them. (Though I will always be in awe of Gibson's stat line for '67 WS: 3-0, 1.00 ERA, 3CG
26K. Not human.)
So my vote will go to Pedro. My fondest memory of Pedro was in game 5 of the 1999 ALDS. The game starts off with 3 innings of wild hitting with a 8-7 score after 3. Then the Red Sox bring in Pedro in relief and all you see on the board from the 4th inning on for Cleveland is zeros. And this was the Cleveland lineup with Lofton, Alomar, Ramirez, and Thome. In my mind, the late 90's Pedro probaby had the best stuff of any pitcher in baseball history. Definitely the best stuff of this era. There will always be pitchers who are more consistent (Maddux) or more decorated (Clemens) but Pedro has stuff that cannot be described with stats or awards alone. You just have to see to believe.
BTW to the person who mentioned Doc Gooden, I agree. Man, what a sad waste of talent. I truly believe he could've been one of the greats. I guess this is just a lesson to all kids ...always in moderation