I've taken the Key West Express and it is indeed about 3.5 hours. You can leave in the morning and come back that evening or stay in Key West for a day or two and take it back. Buying a round trip ticket allows you to use it across multiple days if desired. Its a relaxing ride.
I guess it will matter whether you will be taking your own boat or just taking a cruise boat. I have friends that have taken their own boats and have said travel time and enjoyment will depend a great deal on the weather as high wave conditions will slow you down and be rough going. You can look at area details and things to do on Marco Island on our website http://www.agent4naples.com. I will put some links to the key west boat trip companies.