FYI, terminals C and E are connected post-security (except for gates C40-42 used by Alaska, Virgin America, and Sun Country; there is no Terminal D). The only way you know you've walked from one to the other is a line on the floor -- Walking from C to E you pass gates C10, C9, C8, E1, E2, E3 all sharing one concourse. Domestic-domestic and domestic-international connections don't require re-clearing TSA security any more.

Also, in my personal experience, LY 16 departure usually occurs at gates E1 or E2 (former E1D/E1E?) which are right at the terminal C/E "border" described above.

That being said, I would also choose the earlier B6 flight and longer layover at BOS rather than chance having to wait 48-72 for the next LY 16 flight.