Bayonne Hotels and how many days.

How long do you have altogether?

You can take day trips from each of those three cities. Will you have a car?

What are you interested in seeing and doing?

I stayed in this very nice, well-located hotel in Bayonne this past March: https://all.accor.com/hotel/A0Y1/index.en.shtml

Also stayed at this place in Bilbao: https://www.barcelo.com/es-es/barcelo-bilbao-nervion/. It's really more of a business-class hotel, and not particularly memorable, but good location and very clean and comfortable.

I have stayed in the Hotel le Bayonne - simple but comfortable, and with it's own parking. 10 minute walk along the river to the centre.
Two days enough.

In Bilbao I stayed here =NH Collection Villa de Bilbao. More upmarket but again, its own secure parking. Near tram stop for all attractions.
Three days enough.

Haven't been to SS.

We stayed at ibis Styles Bayonne Centre Gare for a night back in 2017. Ibis is a budget friendly chain. It was perfectly fine and there was an included continental style breakfast. We liked its location near the train station and just across the river from the historic center. We were there on a holiday so parking was free that day. Our room overlooked the river.

I liked Bilbao more than San Sebastian, which is vastly more touristy, but it depends on what you want to see and do. The historic center in Bilbao is larger, and it was not full of tourists in 2016. There are good side trips available from both of those cities, but I don't know what it would be like to drive in and out of them.

What type of sightseeing interests you?

If you do not have a car, then 2 days in Bayonne is fine. If you have a car, then longer, as you can visit the American Cemetery, the Normandy beaches, and other sights not too far from Bayonne.

The Normandy beaches are a 7+ hours drive from Bayonne. They are not nearby by any stretch of the imagination.

I hope you enjoy Bayonne. If you find it boring and unpleasant, as my wife did, take comfort in knowing that the beautiful city of Biarritz is nearby. In fact, you might consider staying in Biarritz rather than Bayonne. They're served by the same airport, and their train stations are served by the same trains.