Barring any problems, the Bugatti Veyron will have a higher top speed than the McLaren F1, that is certain. Unlike cars like the Koenigsegg, the Bugatti has funding and engineering assistance from a major manufacturer and that makes all the difference.
The McLaren will likely still be a better sports car and certainly much more of a driver's car than the Bugatti. It wieghs more than 500 lbs less, and really was designed to be a really rewarding driver's car that just happens to be really, really, REALLY fast. It's a single-minded car built to be the ultimate performance car.
I have no doubt that the Bugatti's straight-line performance, what with its nearly 1000 hp and AWD, but is much more of an ultra-high performance GT car, much like the Mercedes-McLaren SLR but on a higher plane.
Rumor has it McLaren, when the SLR is completed, is going to launch a line of ultra-high performance cars to compete with Ferrari, with an "entry level" car along the lines of the Modena, a GT car (which will likely replace the limited-time-only SLR), and an Enzo-fighter which should finally eclipse the F1.