Bilbao is definitely closer to Santander (it's about 1hr by car, motorway all the way) .. so flying to Bilbao is probably a better option that Vitoria would have been ... Don't know about the buses, but I assume that there are plenty of services
There is also the FEVE train that runs between Bilbao and Santander - [broken link removed] (It's a narrow guage rail service that runs along the north coast of spain ) - The bus is probalby much quicker though !