Hondarribia or St Jean de Luz

The French side feels more different, but Hondarribia is great and easier/faster to get to... You don't want to see both in a day without a car however. I know, I'm not very helpful but but you can't go wrong here. Be sure to allow enough time for a stroll around San Sebastian itself, since you only have two full days.

And there's more to see in Bilbao than in San Sebastian. It is unclear from your question whther you plan any time at all in Bilbao or are just flying to that city. I would definitely prioritize Bilbao over Hondarribia (though I did enjoy Hondarribia). I have never been to St.-Jean-de-Luz.

Hondarribia is closer and I felt it was easier to drive around than St. Jean de Luz. They are not that far apart and if you have a rental car, you could visit both in a day. There is a decent sized parking lot right by the beach in Hondarribia, but we walked to the beach from the Parador in old town. Parking would be easier if going off season. We were in both places in September and had no problem finding parking.

I've enjoyed both Hondarribia and St. Jean de Luz but only swam at the latter location. Staying at Hotel Palacete within the walls of the old town, I did not happen to explore much of new town Hondarribia. If you stay there, you might take a bus at least one way to or from the beach, versus the 2 km walk. Areas of interest in St. Jean de Luz are within a more compact area.

I don't have the newest edition, but a few years ago, the Basque Country chapter in Rick's Spain book did have a page or so on Hondarribia. I liked it a bit better than St. Jean de Luz, but mainly because I think Rick over-hypes St. Jean de Luz. The upper and lower town areas of Hondarribia are both quite nice. Neither one is large, and they don't take long to "see," but you will want more time if you just want to relax, wander, look in the shops (many more of these in St. Jean de Luz), or spend time on the beach (the one in St. Jean de Luz is large; the one in Hondarribia is small and outside of the main town areas).

As for the French side feeling different, I didn't particularly notice that. But be aware that Hondarribia, being just over the border and accessible by boat directly from Hendaye, has a huge contingent of French visitors. When I ate lunch, I was one of the few people ordering in Spanish!

I also agree with acraven - I found much more to "do" in Bilbao than in St. Sebastian, although the latter is undeniably lovely.

Thank you for the responses. I should've been more clear acraven. We have a car, yes, and we are staying three nights in Bilbao first. Drive the whole day slowly through a couple of coastal towns into San Sebastian. I imagine we will arrive mid to late afternoon. Then the two full days in San Sebastian. One to relax / beach / walk around San Sebastian, and one to visit one other town nearby (with our car). I don't know if this changes some of your answers. I don't want to visit two towns and enjoy none fo them, of course. And no, there is no mention of Hondarribia in the latest RS book. Anything you would add based on my now "better framed" question?
Thanks!