I agree with poormom that this is a realistic plan... and also one that is more aligned with your initial desire to visit the Freedom Trail.
One thing to find out ahead of time is when the boat leaves for the Harbor Tour. Still, even if it cuts into the time you set aside for Faneuil Hall, you can always go to the Union Oyster House first and Faneuil Hall second... they are very close.
Both the Old Town Trolley and the Duck Tours give a good overview of several Boston neighborhoods. The big difference is whether you want a close-up skyline view from the water (Duck Tour) or the opportunity to hop on/off at historic sites (Trolley).
And... to poormom... when you make the trip into the city, let me know... perhaps we can coordinate!