The last cost estimate I found for demolishing the garage and rebuilding it underground is from Chiofaro himself, and that was four years ago, He said $180 million.
http://www.bostonplans.org/getattachment/da676067-e92e-41cc-b699-617067342095
I do not know whether that includes the cost of relocating the utility and mechanical infrastructure for the Harbor Towers, which will not be cheap.
So I think $200 million in the current day is a good number.
I have said in the past that I suspect that the garage can't be done away with entirely. The garage was built by the BRA because the BRA was developing a very large, BRA-owned, surface parking lot on which it planned to build three residential towers, though only two were actually built. So Chiofaro, or anyone else, may not simply be able to sweep it away.
Further complicating the matter of the garage is that it serves nearby, maritime-related uses, e.g., the Aquarium, excursion boats, ferries, etc. My understanding of Chapter 91 is that without the garage, Chiofaro gets no relief from height restrictions imposed by Chapter 91; to wit, 55 feet near the harbor, and about 155 feet near the Greenway.
The Commonwealth has determined that awnings, or other protrusions from the side of any building he would build count against the 'open-to-the-sky' provision of Chapter 91's open space requirement. And there is an absolute prohibition of any new shadows on Long Wharf east of the Marriott, so that constrains maximum height.
In essence, his above-ground building must be squeezed into a footprint no larger than 28,500 square feet, have a total building area that does not exceed 900,000 gross sq ft., and is constrained in height by a provision that it must not cast shadows on Long Wharf (about 600 feet).
Thus, any building will be set along the Greenway, that part of the current garage nearest the harbor will be 28,500 sq ft of open space, and the maximum height, if he seeks to try for 600 feet will be at the southwest corner of the site. There will be no grander, expanded 'Open to the Sea' view of the harbor from the Greenway then there is now with the existing garage.
If my memory is correct, they dug up the Atlantic Ave sidewalk next to the garage for the Big Dig, and Google maps, which many not be accurate, shows a northbound lane of the O'Neill tunnel passing under the SW corner of the garage. If this is so, his excavation for a new garage and any building that goes on top will need to shift east by x feet. This shift will lower the maximum height allowed for a new building because it will be closer to Long Wharf.