This is from the BAA's web site. No mention that the course has to be certified. But they don't require that it be certified, it makes a joke of their standards.
To qualify for the 112th Boston Marathon, athletes must meet the designated time standard which corresponds to their age group. Qualifying times must be run on or after September 23, 2006. Seeding is based on qualifying times, which are subject to review and verification. All participants must adhere to the guidelines set forth by the B.A.A., USA Track and Field or foreign equivalent, International Paralympic Committee, Wheelchair Sports, USA, Disabled Sports, USA, and the United States Association for Blind Athletes. Qualifying times must be met in competitions observing these same rules. Proof of qualification must accompany the application. Participants must be 18 years or older on race day.