I'm an MA resident with an LTC and I've flown out of Logan numerous times with guns. Never once has the police or TSA been involved, but just a word of caution that some of the airline employees (particularly at baggage/ticketing) aren't the brightest of the bunch and may not understand the process, so just calmly say "I would like to declare a firearm" and do not bring up your state residence at all (beyond showing them your ID if they ask). Logan is not LaGuardia (which is notorious for arresting people in your situation) so you should be fine.