We just moved to Riviera Dunes in Palmetto. It's on the Manatee River about 6 miles up or so. This is our third marina and we LOVE IT. We selected it based on floating docks, easy access to good "boating" beaches, well inland from hurricane threats and a protected basin (again... hurricanes). Finally, this marina is just 50 minutes from home. I can run down there any time at that distance. BTW - there are tons of great deals to be had at all the marinas so don't be afraid to ask for some consideration.
Prior, we were at Twin Dolphin in Bradenton (less than 1 mile from Riviera Dunes. No thanks - homeless people jumping the gates, walking the docks, etc. More of a party atmosphere, but nice in all other respects.
Immediately prior, we were at Longboat Key Moorings. Pretty pricey. Stuffy people. Beautiful area though, who wouldn't like it? You'll need your bottom cleaned every two weeks in the summer here though and the snow birds will drive you insane in the winter. If it didn't take us two hours to get there, we would have probably stayed.