It's absurd to say that this would have helped Bush. This would surely have helped Gore.
The blame factor didn't kick in historically until, well, years after the actual attack. Nobody between 9/11 and the end of the year was throwing blame about - nobody serious, anyway. It was handled as what it was - a national tragedy. People 'rallied round the flag.'
That said, national security - and the idea that you need someone who was experienced, foreign policy-savvy, etc, would dominate the election. I can't possibly imagine that would benefit a candidate with absolutely no foreign or national security experience, which is what Bush was in 2000. Christ, he only just won as a sitting President in wartime in 2004.
Remember, you only have to throw a few votes in a few states for Gore to win. In this scenario he'd almost certainly win Florida, and, depending on what happens to Nader's vote, possibly New Hampshire as well.
Does anyone have any polls for how the candidates were percieved on the issues in 2000?