‘Which one would you prefer’ is correct in most situations. ‘Which one will you prefer’ isn’t incorrect as such, but it is asking the person to speculate about what they might prefer in the future, not which one they prefer now. In that, future, case ‘which one will you choose’ sounds more natural.

Tom has given a good answer. I would just like to add that 'Which one would you prefer?' is used when asking someone to make or specify their choice immediately. Which flavour would you prefer - hokey pokey or chocolate? Do you know what hokey pokey is, Frank? https://www.italki.com/ana.nz –English and Portuguese Teacher - professora de inglês e português