Hakodate is on my shortlist of places I want to visit in Japan. Hakodate and nearby Aomori are well known for top quality fish and seafood in Japan. So if you go to the morning market, you'll find some great seafood, much of which may not even make it to Tsukiji for wider distribution. Bafun uni (sea urchin), and cuttlefish are among some of the local seafood.
I don't have specific recommendations, but I've just heard a lot about the fresh local seafood, so that's what I would go for. Your hotel concierge or local contacts should be helpful to point you to some good local spots. If you have someone who can help you read through this restaurant listing linked below, it seems like a good resource.