Is GPS considered to be a navigational facility for the purposes of Ops Spec C055?
Yes, a GPS approach can satisfy the criteria of a navigational facility for the purposes of Table 1 in Ops Spec C055.

The FAA gives the following guidance in Notice 8900.218, Alternate Airport IFR Weather Minimums:


  G. 5) Planning for use of GPS-based IAP must be based on a single navigational
  facility when determining the approach facility configuration in Table 1, even if there are two or more RNAV (GPS) approaches to different suitable runways.


This guidance doesn't go to the length of explicitly including GPS in the definition of "navigational facility". However, it does mean that GPS-based IAP can be understood to substitute for a single navigational facility, thereby satisfying the criteria of the first row of Table 1.