I believe "a beautiful pair of shoes" is correct. "Beautiful" is a general opinion (it can be used to describe almost any noun) so it comes before "pair" (which is a noun). Although I would say that neither of your choices would sound incredibly strange to native speakers.

A beautiful pair of shoes - the adjective normally comes before the noun in English. However, you could also say a pair of beautiful shoes...I just think the first way sounds more natural.