The majority of market price difference accounted to PCGS is due to their registration rules for the highest end items. If you are trying to register a top-end set with PCGS they only allow PCGS coins in their registry. NGC allows both their coins and PCGS coins into their registry sets. So I believe part of the difference on the very high end is due to those collectors who are trying to get a high set registered with PCGS that must have only PCGS coins.
If you compare the percentage of coins graded by those two
TPG's for most coins you will find the percentages very close or nearly the same between the two. In other words, if you compare the percentage of MS 64 or MS 65
Morgan dollars you find that both
TPG's are nearly identical in the percentage of coins that will be found in those two grades for the majority of date and mint marks.
The majority of collectors (and some investors who know what they are doing) still buy the coin, rather than the slab, and it makes less difference as to which
TPG has graded and certified the coin. The coin itself will make more difference than the
TPG in many if not most purchases.
Some folks like the LOOK and appearance of one
TPG over another, but that is so split that it's much more a matter of personal preference as opposed to sell-ability.
Most folks would recommend PCGS simply because they do APPEAR to have a better selling base for similar coins. However, if you check the large auction houses, such as Heritage, or the on-line auctions, such as
ebay, you will not actually see any preponderance of preference for one
TPG or another as the prices vary considerably for the exact coin in exact grade/condition.
I use NGC simply because I'm a million miles from a PCGS dealer and I can send my coins in myself with NGC. Plus, I do like the look of their holders, especially since they've newly revamped their labels.