Not sure what's so interesting about that debate. In fact, anyone who's still thinks that it is one is just in denial, at this point. Brady is an objectively superior quarterback. People who think otherwise apparently haven't realized that there are better measures of a QB's skills than career passing yards and TDs (and by extension must think that Brett Favre is the greatest QB of all time).
To note, Brady's last 4 seasons have been:
2007: A historically good season, one of the best of all-time. Consensus MVP, better than any season that Manning has ever put together.
2008: lost to injury
2009: recovery year, still did exceptionally well against a historically difficult defensive schedule (Football Outsiders ranked him as having the #1 overall defense-adjusted QB season).
2010: A historically good season, one of the best of all-time. Only unanimous MVP in league history, better than any season that Manning has ever put together.
If a guy wins 2 MVPs in 3 years, setting major all-time records both times, both times for the winningest team in the league, then he is probably the best at his position. If pretty much every efficiency statistic in the books backs up the notion that he is the best, then he definitely is.