With separate tickets and checked luggage, it becomes a very different story. Aer Lingus seems to have a minimum check-in time of 75 minutes -- "Passengers who do not comply with Check-in Deadlines will not be accepted for travel. They may change their booking up until the flight they were booked on has departed, thereafter it will be treated as a 'no-show' and the booking will be forfeited."

With a 9pm departure from BOS, that means you have to be checked in no later than 7:45. If your incoming flight is exactly on time, the amount of time it takes to get bags delivered and then find your way from Term A to Term E and the EI counter would likely allow you to check in on time. But if your flight is delayed by 10 or 15 minutes, or if your bags are delayed, or if you take a few wrong turns on the way between terminals, you'd be out of luck.