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@RecoveringCowboy 's question.
I know there are better links out there somewhere, but here's a start.
Fifty Years Ago, Jets-Pats Rivalry Began
I just wish the article went further. In the early 1960s the Patriots had a very good team. In 1963 they went to the AFL championship, and the next season went 10-3-1 but missed the playoffs. Two years later the Pats headed into the final weekend on a five-game unbeaten (4-0-1) streak. The one game they didn't win was a 27-27 tie at Kansas City, and seemed destined to play them for the AFL championship. The winner of that game would go on to meet the winner of the NFL championship for the first time ever, in something that would become known as the Super Bowl.
All the Patriots had to do was beat a five-win Jets team. A Jets team that somehow had tied the Patriots in Boston earlier in the season, which resulted in the need to win in the final weekend of the regular season.
Second-year QB Joe Namath, who led the AFL with 27 interceptions that year, threw three touchdowns and no picks, and the Jets beat the Patriots 38-28. Buffalo took the East by a half game over the Pats, and KC ended up playing Green Bay in the 'AFL-NFL Championship Game'.
There has always been a rivalry based on the proximity (less than 200 miles), so many New York transplanted NY/NJ students going to school in Boston, and piggy-backing on the other sports rivalries (Red Sox-Yankees, Celtics-Knicks, Bruins-Rangers) of that time. Obviously it took a big leap when Parcells left New England to become coach of the Jets, but the roots of the rivalry go back much further.