I think both acceptable with slight differences. In n.1 Quali (pl) is referred to good wines. It subtends the word (vini- quali vini) Which ones do you prefer (in general, so that I will suggest you a wine for your dinner)? White or Red?
In n.2 Quale (sing) means wine. We have several good wines. Which one do you prefer (now)?
We have several good wines. Then the waiter asks: "which wines/wine do you prefer?"
I'd like a red wine. Vorrei un vino rosso.
You can also say " Abbiamo una buona cantina di vini, Signore. Gradisce un bianco, un rosso o delle bollicine?" We've a good canteen of wines, Sir. Would you like white or red wine? or bubblies?
Bubblies also I'd like to have "una buona bolla" (slang)
"Aveva in mente qualcosa di particolare?" "Le posso suggerire un...." "Le porto la carta dei vini?" Were you thinking about sth in particular? May I suggest you a.... May I show you the wine menu card?