Madrid or Barcelona?

You need to give us a better idea of your tentative itinerary and your interests. How long is your trip? It can be trickier than expected to move from Portugal to Spain or vice versa. Have you checked on the timing of that leg of your trip?

You plan to go to San Sebastian but apparently not Bilbao. Does that mean you don't care for art (in which case I'd say Madrid is skippable), or is it that you just don't like modern art (in which case you might still be interested in Madrid for the Big 3 museums)? There's never enough time for a traveler to see all the worthwhile sights, so it's always a matter of choosing what is most appealing to you, with an eye to the logistics involved.

Train service from San Sebastian to Barcelona isn't particularly fast, taking roughly 5-3/4 to almost 8 hours. You can check the rail schedule and fares (choose an earlier date for the appropriate day of the week since the Sept/Oct tickets aren't available yet) on the Renfe website. Check Skyscanner.com for flights. There appear to be non-stops available, currently at very attractive prices if you are traveling light, but I just checked for a random Wednesday in late September. Be aware that extra charges for things like luggage can add a lot to the base ticket cost for some short-haul European flights. You'd need to go pretty far into a pretend-booking to find out what the extra charges might be.

The response from acraven is great. If you tell us your whole trip - both the Spain and Portugal sections - we can give better advice.

Take seriously her point about how hard it can be to connect Spain and Portugal in one trip.

Do you like big cities? I do, and enjoyed just being in Madrid. But many don't like it as much as other places in Spain.

Do you like art museums? In addition to the Prado (one of the world's greatest collections), there's the Thyssen, Reina Sofia, Museo Sorolla, and some others. If these aren't of interest to you, your travel time would probably be better spent in other places.

Do you have Rick's Spain and Portugal books? He does a very good job of describing the highlights of Madrid and Barcelona; only you can decide how much time you might want to spend in each.

Have you seen his videos on these places? If not, go to this link, scroll down, and click the country to see all the shows: https://www.ricksteves.com/watch-read-listen/video/tv-show.

I would like to know your full trip plan as well.
My first thought would be to favour Madrid and Barcelona over San Sebastián, especially with an October time frame.

Steak or lobster? I think you would be making a mistake by not visiting Madrid. It has great museums/sites and is fabulous at night. Barcelona is equally attractive - but different with the Gaudi sites and coastal feel. Visit both if possible!

thank you all!
We will be flying to one of the three destinations from Malaga, where we are part of a small group tour.
We join that tour after a driving trip through Portugal, doing a loop that ends up back in Lisbon, We plan on flying to Malaga from Lisbon. This time in question will be the last week of a one month trip, so I'm guessing we will be tired, that is why I am trying to make a good choice here. We do love big cites, and walking in them and eating!. Love architecture. We can get burned out on museums fairly quickly. We are planning on spending some time near the water in either southern Portugal or Spain before out Andalucía tour, so perhaps that will take the place of San Sebastian?

"Love architecture. We can get burned out on museums fairly quickly."

That sounds more like Barcelona than Madrid to me, though Barcelona has a lot of good museums. I especially recommend the Museu Nacional d'Art de Catalunya for the church frescoes and architectural elements rescued from rural churches. I also enjoyed the modernisme collection. There are paintings as well, of course.

I believe the Basque Country beaches are a bit risky by October, though your odds of being able to walk along the boardwalk are probably decent. That part of Spain can be cool and damp even in mid-summer.

Barcelona then I think is the obvious choice.