If you were starting a new organization today, and you could have the farm system of the Boston Red Sox to start your organization, or the farm system of the New York Yankees to start your team, which would you take?
This isn't just a "Jesus Montero vs. Ryan Lavarnway" or "Will Middlebrooks vs. Gary Sanchez" type question. Take everything into account, not just their most recent prospect lists. Think about their minor league affiliates, their recent histories in the draft, what they do on the international front, their coaches and development staff, their philosophies on how to handle young players. Think about their current group of prospects near the major league level.
Think about who they have at the lowest levels of the farm system. Think about their depth (or lack thereof) in both impact talent and depth in future role players. Even think about the commitment of ownership to building the farm organization and the financial and personnel resources that are made available.