hard question b/c there's usally a subjective test of "most fit" based on how fast someone can do a particular sport for a particular distance...
i personally think XC skiing in probably #1 with cycling and running a little behind.
the thing with running is to be an endurance runner you need to not only be fit, but also have durable joints and digestive system. i used to be a runner (mostly triathlete and multisport adventure racing) but then i developed knee and back problems from running too much. it had nothing to do with my fitness.
i think a good argument could be made for triathletes, but again there is then the question of what distance? sprint distance, olympic or Ironman? i personally would say that the long distance Ironman athletes might be more cardiovascular fit, but the top Sprint distance athletes are probably better all-round athletes because they have more fast-twitch muscles and raw strength that is needed in many other sports in additon to their cardio fitness --- now on the ohter hand, someone less fit can COMPLETE a Sprint triathlon while maybe not being able to complete an Ironman, so you must have a higher minimum level of fitness to be a long-distance triathlete.
as to the more generic question of "athletes", a good comparision would be: which sport is the best indicator of overall sport ability? or great athletes of which sport are also generally the very good in most other sports (i.e. better than others in their non-specific sport)?
for example: how do pro football players, road cyclists, downhill skiiers, tennis players, triathletes, soccer players, swimmers, baseball players, and 100m sprinters, high jumpers, volleball players, etc. all do in all other sports? this is sort of the idea behind the decathlon except it was created before cycling existed so only consists of running, jumping, throwing and vaulting... include a few cycling events (track sprint, citerium, hill-climb, time trail, and long endurance race), swimming and a few skiing sports and you might have the defining sport.
the thing is some sports require strength (football, volleyball), some big size (football, basketball), some small size (distance running, rock climbing), some quick speed (sprinting, soccer), some endurance (distance running, cycling) and all require some special skills (ball contact in baseball or volleyball or soccer, trick moves in basketball or football, technical skills like in mountain biking or downhill skiing --- and each requires a different ballance between fast-twitch short-burst strength muscles and slow-twitch endurance muscles -- for example Lance Armstrong's vertical jump was listed in Bicycle magazine as 17" while mine is 36" and we are roughly the same size and weight (i played college volleyball and am a sprint cyclist) - to say that my legs are stronger than Lance's sounds funny, but it depends on the definition at Lance is highly specialized for cycling (in jumping or run-sprinting i am pretty sure i would beat Lance)
with an of course heavily biased view, my vote would go to either Sprint distance Triathletes or XC skiiers or decathletes as some of the most athletic - meaning evidence of most talent and versatility in a variety of sports b/c all require a good mix of both fast-twitch and slow twitch muscles, major cardiovascular enduarance, plus strength and speed.