Even if Boston already had canals they would still need to build surrounding flood protection systems just like Venice and Amsterdam. So why build the canals?
Interior canals can actually make flooding more likely as New Orleans learned when breaks along canals were responsible for flooring the city after Katrina. The solution - as a everywhere else - was beefed up perimeter defenses not more canals. Canals just make the problem harder and the risks greater. Why build a system to deliver vast quantities of water to the center of a city?
The real problem with building reliable flood protection is that it is impossible to fully test and may not be tested by nature for a very long time. This requires sustained effort by level headed engineers and planners not politically motivated dreamers.