The entire "who is the best athlete" thing is impossible to solve, but fun to discuss (for a while, anyway). Clearly Phelps is assisted in his medal haul by the fact that many swimmers can achieve an elite level at more than one stroke, whereas a runner is unlikely to be good at both the 100 and 800. Plus, a runner can train with minimal resources, while an olympic-class swimmer needs to be from a developed country, and (usually) started swimming competitively sometime around 6-9 years old.
My favorite dumb sports argument is whether a 300 game or a hole in one is tougher. Had an actuarial friend that debated that with me for a while over some beers one night. (Consensus was that a 300 game is easier for a pro or a good amateur while a hole in one was easier for a beginner)