Maybe I'm missing something with all the talk of BOS and Terminal C.
That said, 40 mins is enough time to connect within Terminal 5 (T5) at JFK. It is a very simple connection as all flights arrive and depart behind security and you can easily run between any two gates in 10 mins if not less. As you can see from the map, the terminal isn't that big:
http://www.jetblue.com/travel/jfk/
Obviously a delay could cause a mis-connect so, if that happens, you will have to deal with it.
Aer Lingus has a later flight from JFK to DUB (usually departs at 21:00) so, for all you know, they'd just put you on that following a mis-connect. I know they also interline with several carriers so they probably have other options as well.