Thought I'd update this thread in case there was anyone else out there looking for Yoshinkan instruction in the Boston area. I do not believe the Boston Aiki Center is still active as I am under the impression that John Chan now teaches in Hong Kong.
The Goshinkan Dojo recently opened in Newton, MA. It is an affiliate of the AANA and the Doshinkan in Philadelphia. I train there under Josh Nathan Sensei who studied under Utada Sensei in PA for many years as well as at the Yoshinkan Honbu Dojo in Japan.
It's a great environment and I'd encourage anyone in the Boston area interested in Yoshinkan style Aikido to come visit.
You can learn more about the school and contact Nathan Sensei here: http://www.goshinkan-aikido.org/