I have never taken the duck tours here in Boston, but I hear they are pretty good.
There are so many places to go and things to see in Boston, that you would not be able to see them all in one day.
Since an aquarium is an aquarium everywhere you might want to visit Boston Common instead. Walk the Freedom Trail.
I do agree that you should go to Quincy Market. You will enjoy that. If you are a fan of the TV show Cheers, you might want to dine in the Cheers Restaurant.
Have Fun!!