Spent a week in Portugal last November as part of a San Sebastian / Rioja / Galicia trip. Really enjoyed it, especially Porto, even though in general Spain has better food. And even in cases where ingredients are similar in quality, restaurants in Spain seem to treat them better. If you can sneak north to Galicia for a couple of days, you'll likely have some of the best seafood of your life.
That said, Cervejeria Ramiro in Lisbon was probably my favorite place to eat in Portugal. Bustling seafood joint with all sorts of fun sea creatures to eat. If you stick to percebes and various prawn-like things and maybe some Pata Negra, you'll have a blast. Just be specific with qty, so you don't end up with a nasty surprise at the end of the meal, as some of the creatures are quite pricey.
In Porto, O Paparico was my favorite. Somewhat modern with a great wine list. One of the few restaurants with a substantial non-Portuguese list, though after chatting with the somm, we ended up going Portuguese and were happy.
Other places worth checking out: Boi Cavalo, Solar des Presuntos (old school and lots of fun), Gambrinus, O Galito, and maybe one or two of Jose Avillez's places. Thought DOP was okay but people seem to really like it.
If you have time, Sintra is a fun day trip.