My mom and I will be in Marseille for three days in late September. We have a lot already booked, but would love to take a short boat ride. I'm trying to find a 1-2 hour boat tour, harbor cruise, etc. either before 12pm or after 7:30pm on a Friday or Saturday. Any recommendations?
Go to Chateau D'If. It is a castle fort in the harbour just west of Marseille. It is famous for being the prison featured in the "Count of Monte Cristo" by Dumas. It is a story that has been made into Movies and TV Series. I was there myself. The trip takes about 2 hrs and is under $20.00. I don't know their schedule.
We really enjoyed a boat ride from Marseille around the Calanques, and I think that would fit your description. I don't remember which company we used but you can find more info here: https://www.marseille-tourisme.com/en/discover-marseille/nature/the-calanques-of-marseille/how-to-access-the-calanques/the-calanques-of-marseille-by-boat/
The Calanques tour, there's a couple of options on length of tour, difference of a a couple of hours or so which would cost a little more. I did the 2-3 hour ish tour on a beautiful October day. It was wonderful. I also did the harbor tour to the fort on a different day. It's a nice short ride and great view back to the Old Port. (Vieux Port). They all leave from there. You can buy your ticket on line or at the live ticket station by the boats.