I recall one of us having an excellent manicotti dish at L'Osteria on Salem Street in the North End, but that was a few years ago. Their red sauce (as I recall) was one of the best in Boston.
Haven't had manicotti at these places, but they all have excellent red sauce:
Al Dente, Salem Street, Boston
Mother Anna's, Hanover Street, Boston
Rino's, Saratoga Street, East Boston
Lil Vinny's, Medford Street, Somerville