El Morro is a great choice! I was just there last week.

After a 7 day Carribean cruise, we spent 3 days in Puerto Rico. My main reason for extending our stay was to visit the lighthouses there. Unfortunately we only got to see 5/15 of the lights.

El Morro was very nice and is definitely unique.

Cabo Rojo is a shame. Lots of graffiti and vandalism. Spectacular view and location. There are salt flats in the area. Lots of shore birds. Nice beach used by the locals. Lots of potential here. I hope this lighthouse gets restored...