The owners of the J &: E Riggin say the vessel sustained tens of thousands of dollars in damage after lines were cut and the windjammer floated free. The vessel eventually crashed into a walkway.
Police say a 15-year-old boy from Rockland, and a 13-year-old boy from Thomaston are responsible.
They are both charged with aggravated criminal mischief.
Police have also charged the boys for slashing tires on several vehicles throughout the city.
The J &: E Riggin was built in 1927, and was declared a national historic landmark in 1991.