Best waterfont dining in Miami?
Perversely, there are not a ton of good waterfront dining options in Miami. Places on South Beach, even Ocean Drive, generally don't really have water views because they are too low and separated by the street (and besides there is very little good dining actually on Ocean Drive, though BLT Steak in the Betsy Hotel would be an exception).
Possibly your best bet would be Il Gabbiano which has nice windows facing out onto Biscayne Bay. The food doesn't excite me but it is well done Italian. Area 31 does good seafood and is 16 stories up, but you have to get the right angle to really have a water view. There's also Smith & Wollensky steakhouse on South Beach, though most of the place doesn't really do much to tell you that you're on the water. Baleen in Coconut Grove has fantastic views but it has been ages since I've been and my last visit was unexceptional.
Big Fish along the Miami River might be a good spot. It's been a long time (year +) since I was there, but they handled large group (12) of us really well and the food was very good, especially the whole deep fried fish.
It's underneath the Brickell Bridge, I think 5th street.
Not sure if you wanted ocean view, but river view is pretty nice.