We've stayed at the San Juan Marriott several times. You can ask for a delayed checkout. In the event they cannot accommodate you, you can ask that the bell captain hold your luggage until such time as you are ready to leave the hotel.
All the cruises we've taken out of San Juan have left at night, but we've always boarded the ships around noontime. As far as eating goes, there should be a lunch buffet available from about 12 - 4 PM, and dinner should be served at the normal time. Enjoy your cruise!