Boston-based real estate investment trust Berkshire Income Realty Inc. has acquired the Gatehouse 75 apartment complex in Charlestown for $54.4 million, according to a Suffolk Registry of Deeds deed. The luxury 99-unit complex is located at 75 W. School St. in Charlestown, near Boston's North End neighborhood, where it overlooks the Zakim Bridge. Berkshire Communities, the property management division of Berkshire Group, will manage the complex, Berkshire Income Realty said. "Greater Boston continues…