I've done six Bostons and four (or three, I dropped out of one) Twin Cities.
Overall Boston is probably tougher due to the extreme downhill early that beat your quads to death. Then the series of Newton hills that just beat you down. The first of the four is probably the toughest, but they just add up. The one advantage that Boston does have is that if you survive through the hills, most of the last 5+ miles is downhill. Some people have so destroyed their legs that they seize up on the downhill after Heartbreak, which is quite long and fairly steep.
Twin Cities has mostly rolling hills until the river. Getting from the river to Summit Avenue is probably the toughest hill. The problem is that after you seem to crest the hill onto Summit Avenue, it is still gradually going up for quite a ways. A lot of people think that it is flat at that point and don't deal with it well. The rest of Summit Ave is rolling, but the downhill to the finish doesn't really help a lot since it is really steep. A friend who ran it (much faster than me) said that his legs were so beaten up at that point that he would have rather run up the hill.
Both are great races.