Marseille - Parking Advice Needed

It appears there is a public underground garage near the port.:
Parking Indigo
22 Place du Général Charles de Gaulle
13001 Marseille
France

Do not leave luggage where it can be seen

If you would use Google maps in your browser, center on central Marseille, and then type in "parking" in the box to the upper left, parking lots will be indicated with a red symbol containing a white "P." I count about 10 to 12 within a reasonable walk of the departure point for the ferry. Most are run by Indigo or Q-Park, and I've had good luck with both when visiting Marseille.

As noted in the comment above, leave nothing visible in the car. Think like a thief -- not a jacket (might have a wallet in its pocket), phone charger cord (expensive phone might be in the glove box), or shopping bag, even if it just contains a few snack items (might contain jewelry).

Also, if possible, back into a spot by a wall until your bumper gently touches it. Just makes it more difficult to open trunk or hatchback.

Went there recently for exactly what you are doing.

We parked in a large underground pay garage (closest one to the port / ferry)

Seemed like a safe place, we did not have luggage in the car at the time but as a pay garage it did not seem like a place that had any security issues. Making sure nothing is visible and making it more difficult to access is always a good idea in any garage parking lot.

Do not remember the cost, but recall thinking it was not bad.
We enjoyed the day. The ferry ride was really nice (has seating in front if nice out or inside if not) and on the way back stops off at another popular island. We did not stop there but was enjoyable to see something else along the way.
Buying tickets was easy ; as you probably know you have to buy tickets twice ; once for the ferry ride and then again on the island for the prison. It would not be wise to go to the island and not go to the prison as it is the only thing there.

Big Count of Monte Cristo fans so enjoyed the Chateau D'lf ; felt like a miniature version of Alcatraz in San Francisco.
If you have been there you will have a good idea of what to expect, though it is much smaller, older and not as much to do or see.
The exhibits are not to the same level as Alcatraz.
Good views at the top, the place is a mix of an old prison and an old military fort.

Only useful tip I have is regarding food. Have a lunch plan, we did not.
Decided to not eat and caught a ferry right away after arriving in Marseille.

Only place for food on Chateuf D'il was a nice place to grab a beer and sit waiting for the next ferry but did not seem like a good option to eat at and was incredibly expensive for what they did serve food wise.

Upon returning to Marseille we were very hungry and found out every little café, pizza, sandwich place and restaurant that was open when we left was now closed until 7 PM for dinner. Was quite frustrating, we walked for many, many blocks before throwing in the towel and going to McDonalds cause we were starving and everything including small take out places were not serving food. It was summer and the port area was quite lively with some big street performances and the like which we enjoyed.
I was truly shocked about no place open/serving food. All of the outdoor seating places were open but serving drinks and dessert only until 7 PM came and many of them were crowded.
We did not want to stay late as we had a 90 minute drive back to the town we were staying in and preferred to get there before dark.
That was the only disappointment of the day and was our own fault.

Oh' I almost forgot before we left town we went to the Notre Dame Cathedral which I highly recommend doing.
Since it was late in the day we were able to drive all the way up and found free parking on-site.
I am sure earlier it was very crowded but very few people where then when we got there.
No cost to enter and the place is awesome, really impressive church and great 360 degree views.
Definitely worth your time going to.