Shortest regular scheduled service I know of is between Mont-Joli, Qc (CYYY) and Baie-Comeau, Qc (CYBC). The 2 airports are separated by the Saint-Lawrence river in eastern Canada and are separated by 65-70 kilometers (40 miles or so).
At the present time, the route is flown with Air Nova Dash 8s and lasts about 11-12 minutes.
Funny thing is B-727s were operated on that route in the late 70s by Quebecair.. imagine that flight time. The route was also flown by a variety of planes over time including Bac 1-11s, B-732s, F-28s, F-100s, BAE 748s, Convair 580s, ATR-42s and Beech 1900Ds.
By the way, the ferry is 45 miles away from Mont-Joli and it takes 2.5 hours to cross to Baie-Comeau
One of the short domestic extensions I know of is YMX to YQC. For example, there is one Paris flight per week from Quebec during the summer. So, for that flight, the plane's route is YMX-YQC-CDG, and the first leg lasts about 15 minutes and the plane used is mostly the 1011.