As a person coming to do basic molecular mechanisms, I personally prefer Harvard BBS-- a number of outstanding PIs working on very fundamental stuffs: transcription, RNA splicing, DNA repair and translation. Counterintuitively I didn't find many labs doing the same things in MCO. I almost feel most labs in MCO are doing microbiology, neurosciences, bioinformatics and developmental biology. Two POIs (doing RNA biology) who interview me even told me that they would move to other places soon.
You could rotate / do you thesis in any lab in Harvard (even in MIT) regardless of your home program. And I believe both programs provide 3-year funding. So I guess at the end it depends mainly on whether you like a big or a small program, and which program provides courses you like better.