I cannot help you with a route, as I don't ride regularly in Boston.
But otherwise, I would say go for it. Like a poster above mentioned, I find Boston and greater Boston to be pretty bike friendly. While I try to avoid the congested areas, I do on occasion ride through the city and surrounding urban areas. While the roads aren't always in the best of conditions, I have less issues with drivers than I do in some more rural areas.

HTH
zac