Very interesting read. I think that a few subjective terms in the question need to be clarified before the real crux of the argument can be tackled. However, feel free to ignore this post if you are not interested in pedantics and simply want to push the stock of your favourite cyclist. The three terms I am referring are: best; 'one day' and generation.
The former is the central focus of the argument, so I will leave that aside for the moment.
I agree with common belief that 'one day' races do not include time-trials. It refers to one day classics, most importantly (but not exclusively) the Five Monuments; Olympics and World RR Champs (The Big 7).
The definition of a generation is highly subjective. It must be determined both where the time period begun and finished. First of all, does this debate include cyclist's future 'one day' chances? Or is this 'generation' assumed to be over, and we are debating who is the best classics rider of the past generation? I believe the phrasing of the question "who is" is distinctly different from "who will be" thus we only include results which have actually occured, not the possibility of future chances. However, side-notes can be made highlighting the chance a cyclist could 'overtake' another in the coming years. This does raise problems however, because the Northern Classics of 2012 (which favour Boonen and Cancellara) have occured whilst those which favour Gilbert have not. Thus, giving the first two riders more opportunity of success in this 'generation'.
The next question, is when did the generation begin. If we assume that it finished today, or whenever you are posting, then I don't believe it could have started in 2009. Generations typically last longer than three or four years. Simply put, I believe the current 'generation' begun in 2005. Both generally in cycling (with the ProTour & Lance's last Tour) and specifically to these debate (Boonen & Gilbert achieved relatively significant classics success and Cancellara went into PR 2005 as a favourite until his crash).
Thus, I would conclude the generation in question is from 2005 until today.
Therefore, we can debate the real point of this argument - who is the best. Whilst I agree with stated three riders as the main candidates, it is important to remember even within the specified time period, Bettini won the Worlds twice and two Monuments and finished in the top-4 of Monuments a further three times.
Boonen, Cancellara, and Gilbert has made the podium in just as many of the Big 7 races as each other - 4. Whilst Boonen has done it 11 times, Cancellara 10 and Gilbert 8. Boonen and Cancellara have won 3 different Big 7 races, Gilbert has won 2. Boonen has won them 7 times, Cancellara 4 and Gilbert 3. Whilst, all 3 riders have won a lot of slightly less significant 'one day' races during this period. Gilbert other exploits are the most impressive with Fleche and Amstel, whilst not considered Monuments seem only marginally less difficult to win than LBL. The same cannot be said for Gent and E3.
All 3 have significant 'other' reasons. For example, Boonen and Cancellara non-classic success asks if they had focused more on the Big 7, and less on the Tour de France how would they have fared? Second, Gilbert's youth and being midway through 2012 means that the statistics, and outcome, could be different in only a months time.
In short, by sheer quantity - Tom Boonen by a whisker over Cancellara. However, if Boonen manages to win San Remo next year then he will cement his place has the greatest classics rider of his generation.