I've never seen a single left luggage desk at any cruise pier, so I doubt that's a realistic possibility. I don't know Lisbon, but I'd start first by checking the train station. There's much more of a chance to find a luggage desk there.

Nearest train station to the Lisbon port is Alcantara-Mar. Walking distance. Don't recall luggage desk or lockers (wasn't looking for it).

Let's think outside the box here and look at other posibilities. You have quite a few hours to spend before 3 pm so here are some suggestions:

Have you consider booking a private tour so that all your luggage will be in the car while you are touring the city before you get to the apartment? You will need transportation to the apartment anyway; so start your tour at the port and end your tour at the apartment.

Have you consider booking the cruise ship's transfer to the airport or a post cruise excursion so that they will look after your luggage?

Don't remember ever seeing storage at any ports we have been to including Lisbon. Eschew has a good idea about a tour of sorts but that could be expensive and Lisbon is a very do it yourself place.. Also cruise transfer are$$$ as are post cruise tours. Google luggage storage in Lisbon and see what you can come up with..