I don't think it is that simple. Though Jim Koch has been know to eschew strong IPAs, sours, and a lot of the other beers that have gotten big in the most recent craft beer era, I don't think he likes crushing the small competition.
Craft beer has had two distinct eras in recent years, I believe. Samuel Adams was part of the revival, and during the first era that peaked in the mid 90s, Boston did have a handful of decent microbreweries/brewpubs, but they never had a thriving scene. There are certainly a few breweries of note (e.g. Trillium) and the northeast beer scene in general is a major player. There are many, many noteworthy sours, and east coast IPAs (with Heady Topper being their grandfather) are still all the rage.
Part of Honkman's experience may not be that he is not as familiar with the craft beers in the northeast. I suspect, however, that he is seeing poorer selection because the distribution market in Boston may be a lot more constrained, controlled by only a few major entities. He'll probably have to go to bottle shops to find a better selection.