I am a founder of ClubSi and just about a charter member of v6accord.com. I have run both cars (99 Civic Si and 98 Accord EX V6 sedan) at the same track bone stock and modified.
You can see info on my old Si at
http://go.to/redinkracing
My best time in the Si bone stock was 15.88. My best time in the Accord bone stock was 16.1 or so. With just an intake on a cold day, the Accord ran a 15.80, and that best time in the Si was also in sub-50 degree weather. (I never ran the accord with a factory intake in cold weather.)
So it really comes down to the driver, the weather (Accord will probably benifit more as the temp drops below 50) and how long you race (my times are all obviously for the measured quarter mile.) I'd be willing to bet on the Accord on the street most of the time because the automatic makes the Accord driver skill level less of a factor. And as the speeds climb, I think the long legged accord would have an edge over the short geared Si.
Couple more facts...typical chassis dyno numbers for a stock Si are around 138 wHP. And with the short gearing in the Si, the narrow power band isn't that much of a handicap in the quarter. You get into the vtec and the power comes on pretty quickly. And you stay on the vtec all the way through the gears if you shift at or near the redline. With boltons, Si's have been clocked as quick as 14.9 but that was with a VERY good driver and, I think, some good rubber on 15" rims.