Aer Lingus only uses Terminal C now. Emirates left C last year and moved back to E since the expansion had completed. Plus, Aer Lingus only occupies two gates at C late in the day (2PM-4PM, 7PM-9PM) when JetBlue ops aren’t as busy during this time.
The majority of JetBlue’s ops leave during the early morning hours. Every single gate is used for their departures (except 3 gates used by Alaska and Sun Country). It’s so busy between 6AM and 9AM that they even use 4 gates in Terminal E for domestic departure overflow (E1, E3, E4, E5). If you go to those gates in the terminal, you’ll notice that they have signage for the shared gates (C7, C6, C5, C4).
Since 2016, there is now a Terminal C-E connector (between C8 and E1) which means passengers from E can seamlessly transfer to C post-security. So Hawaiian using E still works in their favor and JetBlue’s as they’re codeshare partners. If you come off the Hawaiian flight, you can simply walk to C and connect to your JetBlue flight from there and vice-versa.
I think the timing of the flight plays a role in this. The Hawaiian flight from JFK leaves just before 9AM. There’s probably 4 or so flights that travel to JFK from Boston so the options are limited here. Plus, you have to add times for possible delays both on the ground and in the air, then you have to factor in time for connections so you make it to the gate in time. Timing is pretty tight if you’re trying to get that JFK-HNL flight from New England. It’s just very inconvenient.
By going to LAX, you have a better chance since there are multiple flights from there to Hawaii each day, and not just one like in New York.