Congrats on the new bike Anaphase! I too have just started commuting to work on some of the same streets you are talking about and others I'm VERY familiar with (I used to live in JP and commute to my job in Central Square). Now I live in E. Arlington and ride to my new job just outside of Central on Mem Drive.
Both routes don't seem too bad. The bike paths are definitely a plus, and you really see a lot of cyclists at the inersection of Comm Ave and the BU bridge, but it's still pretty hairy (and scary) driving it, I can't imagine biking it. I would almost choose #2, as long as Market St isn't too bad in the morning, becuase then it'd just be a straight shot once you get on the Charles River bike path.
I have two suggestions:
1. Try both of them on the weekend.
2. Figure out a way home...sometimes it's not feasible to ride the same way home as you did to work in the morning (a problem with my commute).
Also, it says you live in Lowell, did you just move to West Roxbury? And it sounds like you work really close to me in Harvard Square and judging by your screenname, I'm guessing you work for a biotech too. Just curious which one.
good luck!
Emily
It's only worth it if you're having fun