The minute man bike path is definitely the way to go in my book and you'd be joining a good number of bike commuters if you did so. As the weather clears and warms in the Boston area the path gets crowded with joggers and recreational cyclists but depending on the time of day it won't be so bad and it's a beautiful ride. You can then make your way through Cambridge and over the river to the bike path on the Boston side of the river, where you may run into me doing my daily commute into Boston.
I google mapped the bike route and it's actually not a bad route into Boston that it gave- a total of 12.8 miles.
I, too, take my bike with me to cities when I go out of town for work. I do tons of urban biking but I prefer the rides to be a bit more interesting than just a bunch of congested arterials in and out of the city. Riding the bike paths and more scenic routes within cities is often worth the extra time. But if you're short on time and want to blend with the Boston commuting traffic on Massachusetts Avenue and you're comfortable in urban traffic you'll find it quite manageable.