Which one will fit most effortlessly into your schedule? If you're staying at the Wilderness Lodge and planning an EPCOT day, then either would work. When I picked my ADRs I considered all the options near each park, and unfortunately and/or fortunately there were so many restaurants near and in the Magic Kingdom that I wanted to try, Whispering Canyon Cafe didn't make the list. EPCOT has the same deal, except Coral Reef interests me the most of all the restaurants in and around EPCOT. If all else fails, make your decision based on accessibility, because you're going to have people who love and hate both places.
On a side note: If I was taking young boys to Disney, I would take them to Whispering Canyon Cafe, because I think they would enjoy it more, but that's in reference to the boys I know in my life.