Akelare in San Sebastian is pretty amazing. Bonus points to me for the views. It's high up overlooking the sea. 3-star Michelin restaurant by the chef Pedro Subijana.
Other top restaurants (which I haven't eaten at) include Arzak and Mugaritz. One of the great things in San Sebastián is that even in tapas bars or neighborhood restaurants, the quality tends to be high. I know you're looking for a high-end one, though, so those are a few renowned spots.