This is worth checking out over on Grantland, though maybe just scroll down to the conclusion:
That’s correct: Baseball players who accrued at least five qualifying seasons from 1959 through 1988 died at a higher rate than similarly experienced football players from the same time frame. The difference between the two is statistically significant and allows us to reject the null hypothesis; there is a meaningful difference between the mortality rates of baseball players and football players with careers that emulated the NIOSH criteria.
– Bill Barnwell, Grantland
I believe Bill James compared mortality rates for pitchers and hitters in his Historical Baseball Abstract, and found that hitters tended to live longer. If I remember, James suggested it’s because pitchers had more time to drink between starts. I don’t want to speculate too much (he says before speculating), but I wonder if football players do take better care of themselves in the same sort of way hitters take better care of themselves.
Patrick John Flood (blog) 
The Bill Barnwell study is flawed. In order to conduct a mortality study you need to calculate life years of exposure on a well defined group and have a basis for expected deaths (e.g., general population). You may want to read my article on mortality differences in NFL/MLB players published in the July/August 2012 issue of Contingencies Magazine (cut and paste below):
http://www.contingenciesonline.com/contingenciesonline/20120708#pg41