train station in Basel

There are two possible train routes from Basel to Salzburg, via Germany or via Zürich. For the first you could start from either Basel SBB or Basel Badischer Bahnhof, IC and ICE trains to Germany call at both. For the Zürich route you need to depart from Basel SBB. ou should look this up on www.sbb.ch which will show you the correct stations.

There are two different places the cruise ships dock in Basel, eithe St. Johann or Klybeck. Only your cruise company can tell you which it will use.

"is it possible to catch an 08:30-09:00 train?" - that depends on how quickly the cruise ship will let you off. From either berth to either station is ~10 minutes by taxi (cost CHF 30 to 40) or 20-30 minutes by tram (CHF 3.60 per person). Then you still have to allow 10 minutes to find your way through the station, plus contingency.

Or, you could spend the day in Basel and get an early train to Salzburg the following morning.

Following up on the last suggestion above - there is plenty in Basel to occupy most people for a day - or three.

There is the most impressive fountain/mobile/modern art combination with water going in all directions, there is a fabulous toy museum, plenty of good food, several beautiful squares, very easy transport (free if you are staying in Basel) and if you are interested in the city I can list lots more, including a world class zoo.....

There is even reasonable accommodation within a very short walk from the SBB Hbf - we often stay at the Ibis which is next to the station, has good reasonable brekkie and very nice rooms (some with a view) for an Ibis, and it is on a few tram lines for easy access to the centre and the Hbf (and probably your boat).