I've been to Cocoa Beach and Clearwater Beach, and I prefer Clearwater Beach. The gulf is warmer and calmer, the sand is powdery soft, and the sunset over the gulf every night is beautiful.
We stayed at the Hilton on Mandalay Ave, which is a great location right next to Pier 60 Park and pier. (google for info) There were also plenty of restaurants and shops within walking distance to the hotel, then after dinner we would grab a coffee, stay out by the pier, watch the performers, wander through the craft tables, and my son could play on the playground. (I think they charge $1.00 now to acess the pier)
In Cocoa Beach, I liked the actual "beach" and our hotel was nice - we stayed at the DoubleTree Suites. But I didn't find there to be much to do other than walk through RonJon, and you can only do that so many times - especially being from NJ and going to the one in LBI my whole life. There were not many things you could walk to because you were essentially walking on the side of a main road. And I noticed that quite a few things closed early (coffee/gift shops) - I guess because they cater more to the senior/snowbird crowd?
I don't know if it was the actual "section" of Cocoa Beach I stayed in, or if I just had different expectations. I've been to Ft. Lauderdale, Miami, (not near WDW) Clearwater,and Cocoa, and I have to say Cocoa was my least favorite.