Depends on a couple of things. First, how often you have put a foot down on your commute? If you are footing a lot at stop lights, the lower BB helps, especially if you can do it without getting off the saddle. Secondly and this is more subjective, how the bike feels and handles for YOU. I like low BB because I feel like I am riding "in" the bike rather than "on" it. On my old Mercier 300 I can dab with 700x35's. When it is converted to 650b it is really low- 254mm and I need to be careful pedaling around corners, but it rides and handles like a dream for me.
The full suspension bike I had in the 90's was like riding a tall horse and I hated it other than steep downhills.
It really is a matter of preference, but I prefer low BB always.
Ride both on your commute route, a preference will show itself if there is one.
Tom Palmer,
Twin Lake, MI