This question wouldn't have been asked had they found a way to beat the Giants in the Super Bowl. Tom Brady was playing on a high ankle sprain and could barely move. Stephen Neal left the game with an injury.
Their passing offense was clearly superior, but the running game was better in 2004. The injury to Sammy Morris in 2007 was very underrated.
2007 defense was 3 years older and was missing Law and Poole. Samuel and Hobbs had their issues against elite or big/physical WR's. Run defense got exposed when teams where able to keep the game within distance. Colvin's injury also was underrated as now Adalius Thomas had to rush the passer (which he was good at), but was brought in to erase TE's (which he did).
With that all said, the 2007 team was the best Pats team.