My friend Adam did a study of the Red Sox and Yankees and how they've done against each other over the past four decades. I decided to expand that to include the yearly head-to-head matchup between each club, since 1969. (I thought the year the divisional system came into being was a good place to start.)
I also left out the strike years of 1981 and 1994, as those years incomplete schedules were played, so I tossed them out. I did include 1972 and 1995. Games were left off the schedule both years too, but the Red Sox and Yankees played complete schedules against each other those years, so I decided to leave them in. (Also to note that between 1969 and 1976, the two teams were scheduled to play each other 18 times; 1977-78 15 times; 1979-2000 13 times; 2001-06 19 times; and 2007 18 times.)
What I discovered is that the Red Sox dominated the season series over two long periods, from 1969-77, and from 1982-92. In the first one, they won the series every year except 1971, 1976 and 1972 (that year was the only time the two teams have been tied: 9-9). Their most dominant year in the study was 1973, when the Sox went 14-4.
In the other long stretch, the Red Sox bested the Yankees every season but three (1985, 1986, and 1991). The series' were pretty close during that second period, as the Red Sox won six them by counts of 7-6 (and lost one 6-7).
The Yankees have had a long period of dominating the season series since 1993. In those years since then, the Sox have won the series only three times, and ironically two times the Yankees won the World Series (and one time the Sox won it all): 1996, 1999 and 2004. 2001 was the Yankees best year against the Red Sox in this study, when they went 13-5. (One game went unplayed that year: the rainout at Yankee Stadium on the night of September 10.)
Overall, the Yankees have won the season series 19 times, the Red Sox 17 times, along with the one tie (not including the strike years). Before 1993, it stood at Red Sox 14, Yankees 8, with 1 tie. So you can conclude the Sox dominated the Yankees in the season series until the "Joe Torre Era" began, where the Yankees have gone 11-3.
I also compared the head-to-head matchup to which team had the better overall record. The Red Sox have had the advantage in both in the years 1969, 1973, 1975, 1982, 1988, 1989, and 1990. Ironically, in none of their last three pennant years of 1986, 2004 or 2007 did they win both. The Yankees won both twelve times: in 1976, 1980, 1985, 1993, 1997, 1998, 2000, 2001, 2002, 2003, 2005 and 2006.
In the overall matchup between the two clubs, the Yankees have won 292, the Red Sox 285 games, since 1969. That does not include postseason games, but does include the 1981 and 1994 strike seasons. If you take out those two years, they are even closer: Yankees 282, Red Sox 279.
So, despite the Yankees dominance since 1993, the two teams are incredibly close in the overall matchup since 1969.
Just something to consider on Super Bowl Sunday. When the final whistle blows, baseball takes center stage again.