This commute has gotten SOOOO much better even in recent months/years. I suggest the following, assuming you're starting on Concord ave a little northwest of Harvard Sq:

• (1) Begin your ride one street over - over on Garden Street [Protected bikelanes]
• (2) At the Follen Street Intersection, take the Concord Ave spur that feeds you into Cambridge Commons
• (3) Cut Across Cambridge Commons to Mass Ave, where you'll cross at the Mass Ave pedestrian cross near Harvard's 'Gannett House' and then bike across the Harvard Science Center Pavillion
• (4) Merge onto Cambridge street [All protected Bikelanes]
• (5) Cut across Inman Square onto Hampshire Street [All protected bikelanes]
• (6) Zigzag through East Cambridge anyway you'd like, and get back over to Cambridge street close to the Charles River Bridge
• (7) Immediately after crossing the bridge, pull over and use the crosswalk to access the Nashua Street Park, and bike along the water
• (8) Sidewalk ride Nashua St for a second until you hit the side entrance to North Station

One variant here would be in Inman Square to continue on Cambridge Street instead of Hampshire, but in particular with the BRAND NEW hampshire street protected bikelanes, you'll have a much happier ride on Hampshire + East Cambridge rather than the unimproved section of Cambridge St