A spill from this proposed lab is "virtually inconceivable." That doesn't mean it won't happen. And something about doing research with dangerous bioagents in a major metropolitan center just seems like a bad idea.
Look at it this way. It might triple the cost to move it a few miles away from Boston, into one of the sparser areas. Compare that to the cost if an outbreak occurs where 16G people are crammed into a square mile. Tight quarters make such things spread more quickly. It seems to me, that planning for the worst case scenario, you'd want to avoid such a crowded area.
They want to draw people who work in Boston- but most professionals working in Boston don't live there. They live in the suburbs. So they'd have to commute anyway; most urbanites don't think a 45 minute commute is anything. Put it in a less crowded suburb. At least that way, there's a chance of containing the outbreak, should it occur.