I might be biased, but NYC-DCA(ish) is pretty well served by Amtrak. Getting to DC from Boston? Even the Acela isn't that much of an option. Heck, going anywhere beyond New York from Boston on Acela, the price jumps DRAMATICALLY (I have daughters in Philly and was shocked at the price jump of BOS-PHL compared to BOS-NYP).

That could be a reason why Boston's connection to DCA is hanging around.