What if we got hit by a category-4 or category-5 hurricane? It happened in 1938; so it's not out of the question:
Several survivors along the coast of Rhode Island, stated that at the height of the hurricane, they saw a 40-foot fog bank rolling toward the beach, when the bank got closer, they realized it wasn't fog - it was water.
To be sure, Boston is not a bowl below sea level, good parts of the city and surrounding area consist of hills (I'm typing this on Grew Hill in Roslindale, high up in the clouds at 200 or so feet above sea level) and, overall, there are more escape routes out of Boston than New Orleans. But what would happen to waterfront areas (from the North End to East Boston to South Boston)? The areas along the Charles River Basin? Take a look at this relief map from the US Geological Survey's National Map:
Imagine a 20-foot wall of water hitting that. And while the city as a whole is not underground, key parts of our lives are: Remember how long the Kenmore stop on the Green Line was out of commission when the Muddy River flooded a few years back. Now multiply that by all the subway stops and tunnels downtown (well, except for Charles/MGH). The Big Dig. Basements, parking garages, utility conduits, you name it.
Perhaps equally important, what would happen to our social fabric? Would our police maintain order instead of rushing into the Wal-Mart to pick up some DVDs? (John: At least we know that there won't be a Wal-Mart downtown to loot). Would administrators at Children's Hospital be forced to take up arms?