Thanks for making the adjustments I pointed out.
My personal suggestion--since you say you like gameplay such as Charleston, Vancouver, Luxembourg, etc.--is to make the gameplay straightforward and not incorporate anything "cartoonish" in the actual gameplay. Meaning, no Duck Boat as a territory and no weird -1 bonus or bombard for Beacon Hill.
Instead, I'd incorporate landmarks and other "Bostonish" material into the background and the color scheme. You might want to take a look at another small city map in development, London, to get some ideas. If a territory in the Harbor is need, maybe just "Harbor" as a water territory (like Sea of Japan on the Japan map). You might still use the Duck as an icon, but I'd tone down the cartoon nature of it. On the other hand, you could use the USS Constitution as the water-based icon as it does sail from port once a year.
I think, with some blended in icons like a silhouette of Paul Revere, an oldish American flag, the Old North Church or other similar items you could couple them together with an aged red/white/blue & brownish/sepia theme and have something really awesome here. Basically a present-day geography Boston map, but with a nod to its 1775 era.
All of those are just suggestions, though... you could take this in a number of different directions and you might want something more like Portland, where icons and landmarks are part of the gameplay. That just happens to not be my cup of tea, no pun intended.