Hard to say, ages of kids? Do you want a buffet or full sit down meal? Are you on your trip and say that you've already been to Cape May or is it just a plan?
If its just a plan, then I say go with both of the others as Chef Mickey's is just so classic Disney. We will be back there on our next trip. It was my nephew's #2 most favorite thing at Disney. Mickey, Minnie, Goofy, Pluto and Donald were there. The monorail overhead and the napkin waving, a lot of "entertainment" was had by all! I would say we made the best family memories here.
He also loved the tanks at Coral Reef and he ate very well there (bread, apples and pizza). We were all starved when we arrived for lunch and joined the clean plate club there!
Bottom line, both are good and will likely entertain your kids. I will strongly suggest that if you are not seated next to the tanks, don't allow your kids to squeezed between tables of diners to get a closer look. That seems to the biggest pet peeve of Dissers dining at Coral Reef. We sat up in the middle section and had a great view of the tanks. My mom and nephew did walk down to the lower level, but nephew did not go between tables of diners to get up to the glass. One thing for sure you will be able to relax more at Coral Reef, its a more serene atmosphere and someone is waiting on you. No taking the kids up to the buffet, managing portions for them etc. I think its alright to treat yourself to a bit of a timeout too!