We went to Marco Island last March for a convention and loved it. Thing is though, there really isn't much to do other than the beach. We went to Naples when I was pregnant with my daughter, so we knew that area a bit and did spend some time there, but other than the zoo (which is really tiny) and the alligator stuff, there isn't much. We went to the mall and looked around the pet shop if that says anything. Naples has a cute little strip with shops and restaurants, but nothing to spend a day on or anyting. The zoo is about 2 hours, same with the gators (and my daughter LOVES alligators, sleeps with a stuffed one since she was a year old, and still didn't take up a full day for us).
In Marco Island we stayed at the Marriott, which was great cause it has a waterslide, fountains and buckets and stuff that dump on you at the pool, a kids club that had some fun activities, big arcade, and a great beach. But my kids are water bugs and can stay in the pool/beach all day and be satisfied. The only thing we really did on Marco Island was get my daughter's hair braided and eat at a couple of restaurants.
In Naples we stayed at the Ritz on the beach, which was great. Beach wasn't as nice as Marco, and the pool wasn't either, but way more restaurants in the area to choose from (the Marco Marriott had a bunch, but none were really great and breakfast kinda had to be buffet, which was annoying, or the coffee shop), and chain restaurants which can be good when you have small kids cause you know what they'll eat and stuff.