It depends on what you're looking for. I would say that the best place hands down is The Waterfront Grill. But be prepared to have a big dent in your wallet. Dempsy's Brewery right next door is pretty good, is also on the water, and doesn't cost as much. Mcnears Saloon right across the river from these places makes a great omlette and has an extensive menu for both breakfast and lunch.
Those are the only places I have been to, but I never left any of these restaurants unhappy. And the best thing is that all of these restaurants are real close to where your boat will be docked.