I believe there are only two big corporations still headquartered in Boston (and even one of them is sliding stuff into NH because its advantageous from a tax standpoint to do so). The rest have left, because of mergers, greener pastures elsewhere, whatever. (And this is why new towers for commercial tenants aren't being built, and probably will only be rarely built in Boston in the future.)
And with all the sanctimony and wringing of hands, maybe Bostonians ought to repay the Federal government and the Federal taxpayer for the tens of millions the Federal government spent on infrastructure for the Charlestown Navy Yard for the benefit of the BRA and developers.
Let's see if we can make a count of major corporations headquartered in Boston:
(in no particular order except mostly alphabetically)
1) Fidelity Investments -- not going anywhere from P.O. Sq.
2) Putnum Investments
3) American Tower
4) Au Bon Pain
5) Bain & Company & Bain Capital
6) Bentley Motors (U.S. headquarters)
7) Boston Consulting Group
8) The Gillette Company, div of Procter & Gamble
9) Houghton Mifflin Harcourt
10) John Hancock Financial Services, Inc, the United States division of Canada's Manulife Financial
11) Liberty Mutual
12) New Balance Athletic Shoe, Inc.
13) Sonesta International Hotels Corp.
14) State Street Corporation
15) Wayfair
16) Zipcar
17) Vertex Phamaeuticals (not quite yet)
18) Boston Brewing -- Sam Adams Beer
19) Boston Red Sox
20) Boston Celtics
21) Legal Sea Foods
22) Partners Healthcare -- Mass General, Brig & Womens, etc.
23) Boston University
24) NSTAR
25) Blue Cross Blue Shield
there are quite a few more who employ over 1000 people and are either a Hq (absolute), a North American or US Hq, or divisional Hq (such as Gillete)