After seeing the rumor posted on Twitter and LiveJournal, I just now phoned the store to confirm. Liquidators are taking over the store on July 1. The store was unable to renegotiate its lease with the landlord under Chapter 11 bankruptcy.
This will leave no new-book stores at all in Downtown Boston. Barnes & Noble closed a block away in 2006.
(x-posted to b0st0n LiveJournal)