We have 2 night’s available at the tail end of a river cruise from Amsterdam to Antwerp. Which city should we stay in?

You can stay in Antwerp and do day trips out to Brussels or Ghent. They are all close and there are good rail connections. Antwerp is a pretty city, you won't regret it.

Lavandula

Stay in Antwerp. If it's only 2 nights, that is one full day. You can see the hightlights; Rubens House, Red Star Line Museum, Cathedral - and wander around the old town.
I don't know what your interests are, or from where you are flying back. Are you returning from Brussels? That is easily reached by train from Antwerp.

if you do stay in Antwerp, be sure to see the train station - it’s fantastic

I'm a big fan of Brussels, but stay in Antwerp. Lovely, lovely, manageable town, and if you want to go to Brussels just hop on the train.

Brussels. But I'm peculiar that way

I would say Antwerp! Such a pretty place with many sights to see!

We liked both, but I'd choose Antwerp for two nights. Brussels was busier and more touristy, while Antwerp had a more convivial atmosphere. There was plenty for us to do and see there, and it's about 30 minutes to Brussels by train. Brussels Centraal is walking distance to the Grand Place, so you could easily go there to see it lit at night.