You will be asked to vacate your cabin around 7:30 to 8:00. You can take your carry-on and go up to the dining room (I don't remember if the Windjammer is open) to eat breakfast and then hang out somewhere in a public space until your color is called, or if you want to hang around till the very end.
They have to get the ship ready for the next week's cruise.
There is a restaurant over in Old San Juan (http://www.barrachina.com/
)that will hold your luggage for you if you want to do a self-guided tour up to El Morro and OSJ, and I think the Wyndham will store your luggage, too.
This could be an option.
I believe you cannot check into the airport more than 3 hours ahead of your flight, so you do need to find something to do.
Have a great cruise!