For Isabela:
Uma's. Right at Jobos Beach. Everything I have tried on their menu has been great. Mediterranean and Eastern European dishes for the most part.
Tsunami's is more of a sport bar, also in Jobos, but great food.
La Chancleta de Maiz. A food truck (mostly Mexican fare) located closer to downtown Isabela. Close to the Econo supermarket. Open late for that midnight snack.
La Vista Smokehouse. As mentioned, great views of Jobos Beach as it sits on the cliff. Slightly sweet BBQ, but good. I like more heat on my BBQ, and more vinegar.
Aguadilla:
Del Romano is the name of the smoked pizza place mentioned previously. Have not tried it yet, but from the pictures on Facebook, they have it together. They operate out of a modified shipping container, so should be easy to spot.
Arecibo:
Salitre Meson Costero. Great seafood restaurant right on the beach, just east of the Arecibo lighthouse, jest west of the Christopher Columbus statue. Also very close to Cueva Ventana.
Aguada:
Guayabo's Tropical Sunset. Seafood spot right on the water. Full menu and great views.