Only the underground portions, which is considerably less than the entire 103 mile system. Above ground, they can use traditional cell towers. Grand Central's tunnel is wired too I believe. I found my cell to work, not well, but still, in some of the tunnels on the T. In addition, as with Washington, the above ground portions needn't be wired and in that way. Knowing the T they will likely spend the money anyway to wire thigns like the Longfellow Bridge, or the outer tenticles of the the Green line, or the Blue Line.
Further, a cellular bomb, if u will, since they could work in open air, could be used on an elevated portion anywhere, such as in Chicago, New York, Washington, or scant portions of Boston.