Not a Boston resident, but have some friends up there who say that there are great bike paths for urban ingress/egress, but not particularly good for intra-urban travel. Does that match your experience?
I've put on about 200 miles since moving to Boston, and that observation does not align with my experience at all.
So far I've ridden one very good path connecting a few suburbs to Boston (Minuteman Bike Trail, a rails to trails path). There are other paths, but they're combined with running/walking trails and generally not conducive to bicycle travel.
The bike lanes of nearby Somerville and Cambridge are okay, but still lacking in comparison with Minneapolis.
I think my friends were riding along the Charles River, for what it's worth. They're more occasional bike commuters (once or twice per week) than a real serious bunch, and I don't know their start/end points.
Rail-to-trail appears to be how most longish (10 mile +) bike paths come into existence in the northeast, from my observations. There's a lot less "free space" to work with than other parts of the country, since the land is so developed / dominated by automobiles.
I used to commute on the Charles River bike paths and esplanade. It is actually pretty great for commuting from the Allston and Harvard areas downtown, but that experience doesn't generalize to other routes around the city. And the last half mile or so to get to your actual office can be pretty perilous.
