I don't know anything about "Arbolagaña" in the Museo de las Bellas Artes, although the museum is really worth a visit, maybe even more so than the Guggenheim IMO, at least the actual exhibition, not the exterior.
But I had dinner at Etxanobe last night and it was very good. We were lucky since it was a very mild night so we could sit on the terrace and the views are spectacular, since the restaurant is on the 3rd floor of the Palacio Euskalduna.
By the way, it's right across from the Hotel Melia and just a few minutes walk from the museum (Bellas Artes) through a small park, also other hotels like the Gran Domine and Miro are only about 10 minutes walk away.
We had the "Conozca el Etxanobe" menu which is 7 of their most known dishes and there was not one that disappointed, some were really really good.
They have a smaller menu as well and one can eat a la carte, they even bring an IPad to the table to show you the different dishes (might be a bit much for some, but at least you'll see what you get).
So if you can, try to have dinner there, otherwise I'm sure lunch will be just as good.
Hope you'll enjoy Etxanobe, as mentioned, I did really like it, but it's definitely more on the "traditional with modern touches" side.
May I ask where you'll have meals in San Se afterwards?!
We are there right now and had lunch at Etxebarri yesterday and dinner tonight at Martin Berasategui...