Cook and Fournette against Common Opponents:
2015:
Cook - Florida, 26 Rush, 183 Yds, 7 avg. 3 Rec, 11 yds, 3.7 avg
Fournette - Florida, 31 Rush, 180 Yds, 5.8 avg. 1 Rec, 15 yds, 15 avg
2016:
Cook - Ole Miss, 23 Rush, 91 yds, 4 avg, 7 Rec, 101 yds, 14.4 avg
Fournette - Ole Miss, 16 Rush, 284 yds, 17.8 avg, 3 Rec, 25 yds, 8.3 avg
Both played Florida, but Fournette got injured during the game.
Cook and Fournette against top 20 defenses (2015 and 2016):
Cook - 2015: BC #2, 15 Rush/54 yds, 2 Rec/3 yds; Louisville #11, 22 Rush/163 yds, 4 Rec/60 yds; Houston #19, 18 Rush/33 yds, 2 Rec/26 yds
2016: Louisville #9, 16 Rush/54 yds, 1 Rec/8 yds; NC State #3, 18 Rush/65 yds, 2 Rec/17 yds; Boston College #5, 18 Rush/108 yds, 2 Rec/12 yds; Michigan #13, 20 Rush/145 yds, 3 Rec/62 yds
Fournette - 2015: Alabama #1, 19 Rush/31 yds, 0 Rec; Arkansas #12, 19 Rush/91 yds, 3 Rec/36 yds;
2016: Alabama #1, 17 Rush/35 yds, 1 Rec/8 yds; Wisconsin #4, 23 Rush/138 yds, 3 Rec/38 yds; Auburn #20, 16 Rush/101 yds, 2 Rec/4 yds;
The stats show players that are very talented and fairly evenly matched. I give the overall edge to Fournette for a couple reasons. First, in 2015 and 2016 Florida St.'s passing offense ranked 39 and 33 in the NCAA. Pretty good, but not amazing. LSU's ranked 108 and 101, aka pretty awful. This allowed defenses to stack the box against Fournette twice as often as they did against Cook: Fournette, 7 defenders or less 33% of time; Cook, 7 defenders or less 60% of the time. And finally, Fournette injured his ankle in the preseason, but because he's all LSU had to offer they kept trotting him out there to get it reinjured in the Wisconsin game and Auburn game instead of letting it heal properly (yes, he'll have to deal with this in the NFL as well) but even injured he put up good stats for half the year in 2016.
We won't know for a couple years who ends up being the better NFL player, but if they wound up in similar situations, I'd put my money on Fournette.