Wiki says that Sonic's speed is faster than the speed of sound. The Flash, on the other hand, can vibrate through walls and is apparently capable of traveling through time if necessary. In animation, Flash is so fast that he can be in front of someone one second and beyond them in literally the next second after that. I don't think Sonic ever did that. Also, in the games, Sonic builds up momentum before he really takes off. Flash doesn't.
I have no idea what kind of stuff Super Sonic does in the Archie comics, but by default I think Flash wins this easily.