Hmm i know this was asked as a general question, but several details could tilt it either way.
Loadout/Armaments
If all things were equal, both geared for A/A, i would assume the f15 would have an edge. With most aerial encounters happening out of los, with amraams, the f15 would prob have a better shot against the missle, and then closing for a kill.
Variants
Again it would matter which version would be up against which, but against the latest eagle and the superhornet, i think i give the edge to the hornet. One factor no one mentioned about the new models, they have enhanced stealth and infrared signature suppression. Im not sure if its alot, but again it would aid in its ability to survive the first salvo against the super long range missles. Also the superhornet is supposed to have along with the better avionics, better integration with some sort of future "battlenet", with closer ties to the awacs planes. This could give it an edge with the initial engagement, possibly engaging sooner with better data. With enhanced "stealth", could also buy it some more time against the eagle.
Honestly i think its a wash. Any of the above factors, along with a dozen others could favor one or the other.