I would say CR over Brae Burn, but they are both great experiences. BB has a bit more historical "special" feel than CR, but CR is the likely better golf course. I'm also a huge fan of Essex CC, which I think is slightly more fun than Myopia when deciding b/t the two.
I lived in Brookline from 5/05 to 6/06, so I've driven to many of these courses from there.
I'd say Logan is 20-30 mins from TCC, probably 50 mins-hr from Essex. Taconic is easily 2.5+ from Logan, probably closer to 3 hrs.
Out of your "Boston courses<30 mins from TCC" list, I would say Granite Links and Blue Hill are just outside 30 mins, but the others are inside.
Of course if you are trying to get anywhere from 7-9 AM or especially 3:30-7 on a weekday, good luck. I bet Logan to Taconic starting at 4pm from Boston (on a weekday) would get you out there at about 8-8:30 pm, and to Brookline at 5-5:15.
That is a great list of almost everything worth playing in MA. I would only challenge Chicopee (definately not if its the Municipal course) and Maplegate (debatable) as not being worthy of the others on the list. I think by my count I've played 33 of 53 on your list.