Will be in Brussels in late May/early June and would like to visit either Gent or Antwerp (using public transportation) as a day trip. We've been to Brugges (although it rained heavily on that trip, so we're planning to return). We've also
booked a full day trip to Luxembourg.

Which city would be recommended to visit?

Gent. Not even close.

Ghent for sure for me - though some people really seem to love Antwerp. I didn't.

I loved Antwerp, but if given a choice I'd say Ghent.

Both are good. If you have specific interests one may be better than the other.
I would do one day in Gent and one in Antwerp and skip Luxemburg, but that's just me.

We really liked Ghent and found it to be more 'real' than Antwerp or Bruges, and not as busy as the latter. Most things can be seen in one day. The Adoration of the Lamb is there too if you're into that.

Gent is smaller than Antwerp and thus easier to explore for a day - Antwerp's is great too but some of its gems are outside the town center - like its renown Art Nouveau areas. Most will IMO like Gent better overall rather than much larger Antwerp.

If you mean Luxembourg City, I'd agree.

Luxembourg City is rightly IMO panned by many for being boring - in architecture and looks but it is awesomely scenic from having a deep gorge run right thru it - the first city I ever went to in Europe I was floored by how cute that was - but there is a paucity of must things to do - you can tour the casements or tunnels hewn of of the steep cliffs thru the ages for military purposes and trek out to suburban Hamm for the U.S. Military Cemetery/Memorial where General George 'Blood and Guts' Patton lies buried, after being killed after WW2's conclusion in a jeep accident in the Grand Duchy.

But yes if I had to chose between day trips from Brussels by group or solo I'd pick Antwerp or Gent or the Namur/gorges area first. And yes the Grand Duchy of Luxembourg outside the modern capital is very very cute - if the tour includes some of that like lovely Clervaux and other rural areas then that would be different. But just Luxembourg City I agree with Andrew.

I ditto what StCirq said--both lovely, Ghent more fun

Antwerp has some worthy museums for sure, and that aspect alone would make it well worth a visit for many. But it just wasn't especially charming compared to Ghent, which oozes charm without the tourist mobs of Bruges.

Gent by acclamation!