Carmen Thyssen Museum or Museo Nacional Centro de Arte Reina Sofia

Depends on your interests. Reina Sofia is modern/contemporary art and holds Picasso's Guernica, Thyssen-Bornemisza has a wider historical range.

I would suggest looking at both websites to see what is in the collections.

I went to both and enjoyed both. Guernica is certainly stunning and worth seeing, but the Reina Sofia is huge and takes a lot of time to get through and had a fair amount of art I wasn't super interested in. I'd check their website and see if they have any special exhibits.
The collection of the Thyssen is more my vibe overall and the museum size felt very manageable.

Those two museums are not large. Visit both and only visit their highlights.

The Reina Sofia because I'd want to see Guernika.

I’ve only been to the Reina Sofía. The last time we visited it was during the free admission hours.

The Thyssen-Bornemisza Museum has an amazing collection, including masterpieces spanning time from the Renaissance to Post-Impressionism Only the best works are on display, making the Thyssen one of the most enjoyable art museums anywhere.

I enjoyed the Thyssen more, personally. I did both in the same day but could’ve stayed a lot longer at the Thyssen. I wandered around the Reina Sofia after appreciating Guernica (which is impressive, for sure) but didn’t find much else to catch my eye. I’m not a big modern art person.

If you want to see Guernica and don’t mind coughing up another admission fee you can always speed run the Reina Sofia to see Guernica (assume the room will be crowded) and then head to the Thyssen for a more leisurely tour.

With so few days and already going to the Prado (overwhelming in its own right) you might be art-ed out. But I agree picking one over the other depends on your particular interests. I loved the Thyssen but also appreciated seeing Guernica at the Reina Sofia (I did go to the latter on free admission day). If you want to keep your options open, you can get a pass that covers all three museums and save a few euros https://www.museoreinasofia.es/en/visit/opening-hours-and-ticket-prices/paseo-arte-card

The Thyssen was far more interesting than the Sofia. At the Sofia, besides Guernica, we enjoyed some lovely and conventional Dali portraits in an adjacent room. The exterior stair/elevator at the Sofia was more impressive than many of the exhibits. Do not skip the Prado - one of the wold's great museums. If you don't have much time, checkout RS highlights and hit only the 'biggies'. Their main cafe is very good, also. The 3 museum pass is cheap and allows faster entry.

Try to see both.

These two wonderful museums are less than a kilometer apart and they are on the same street
See them both - manage your time and enjoy Madrid. One could see all three (with The Prado) on the day of your Prado guided tour. That's a lot of art to digest - the stuff that dreams are made of.