It depends if it is a business or leisure trip. Also how valuable is time vs. comfort for you?

If you are on a leisure trip and value comfort, then definitely the second option. You may be on a leisure trip, but value time, then the first option.

If you are traveling on business and have time to relax, then second option, so you can get a good sleep on lie flat seats and take a shower at the DL lounge at JFK and take your time in connecting to Boston.

If you are on business, but have a pile of work to do on the date of arrival before the event later in the afternoon, take the non-stop flight to save time.