Indeed both are possible due to the potential form of いただく heading the verb.
That said, I think が is very slightly more natural here, because you don’t really want to focus on the customer and the fact they can choose drinks (which feels very slightly less polite), but rather the drinks and the fact they can be chosen by the customer.
I just used the passive to show that in English, but in this Japanese sentence it can be done by using 〜が on the drinks (and 〜に on the customer), resulting in a similar syntactic structure to what a passive would be in English (where the grammatical subject is the drinks and the “by ...” is the customer).
If you use 〜を on the drinks, the fact the “subject” of 選ぶ is the customer feels emphasized — even though the customer still gets marked by 〜に due to いただく, it feels like there is a missing/floating 〜が which marks the customers somewhere lower down in the syntax tree (even though there isn’t?). Either way this arrangement doesn’t feel as polite/distant to me. It feels more like it’s highlighting the customer’s volition.
That all said “〜をお選びいただけます” is a perfectly valid form and this is all a bit too subtle to be certain about...