Neponset river trail and along the harborwalk to Castle Island. Through Southie ( Seaport Blvd has bike lanes and can be interesting but lots of traffic, Summer tens to have less traffic until you get near South Station) across the Channel up the Greenway around Atlantic Ave through the North End cross North Washington St then take a right on Beverly St just before the Garden work your way over the Charles river locks and into Paul Revere Park where you can ride over the newest (and far coolest) bie and pedestrian bridge in town to the Museum of science.
Google Maps has a bike icon if you select directions to help you map this.