Honestly, I have to rank the 2004 WS higher.
2001 Patriots was a 6 win turnaround following the loss of the franchise QB. It was also a major upset over a heavily favored SB opponent, and really sent the two franchises in opposite directions. But imagine this? If the Pats win that game, then don't go on to win two more and become a dominant team in the decade, does it matter as much? Sure, it was a great moment, but if it was one and done, and we had more seasons like 2002 (9-7, no playoffs), we'd revere it the same way we do any one-hit wonder. The moment itself doesn't stand up as much without the subsequent success.
2004 Red Sox have so many things going for them in this regard. First championship in 86 years. Not only beating their hated rival (who, despite the comment about Red Sox payroll, had an even higher payroll by far), not only hobbling out a bloody sock Curt Schilling, but beating becoming the only team in the history of baseball to come back from 3-0 down. That simultanesouly made the Yankees the biggest chokers in baseball history.
Anyone who followed that team all year, from the Nomar trade, to the 19-6 drubbing in game 3 of the ALCS, watched every game of that series without breathing. The extra innings HR by Papi, every game (save game seven) coming down to the wire. I remember driving home from work during game six, and hearing the A-Rod slap play in the car, then running in from the driveway parked diagonally to join my buddies to see what the hell happened!
It was one full week of pure, unending tension, that suddenly lifted the collective weight of GENERATIONS of boston sports fans from an 86 year old drought.
I love the Patriots, probably more than the Red Sox, but I can't top that memory with anything thus far. 19-0 would have been close, but it wasn't to be. 2004 was quite simply the most memorably story in Boston sports history.
