The mishap that stranded a Boston Harbor Cruises whale watch boat on Monday will likely cost the company nearly $100,000 as it reimburses passengers for the snafu. The Cetacea was supposed to return to Long Wharf at 4:30 p.m. Monday but a propeller became entangled in a ship mooring line as the boat was returning to Boston. Sheila Green, a spokeswoman for company owner Nolan Associates LLC, says the boat became stranded about 14 miles offshore. BHC sent one of its boats to retrieve the passengers,…