Does the Working Set Paging Algorithm use a separate page table?
Denning provides a rough definition for a working set in Section 2:


  Roughly  speaking,  a  working  set  of  pages  is  the  minimum 
  collection  of  pages  that  must  be  loaded  in  main  memory  for 
  a  process  to  operate  efficiently,  without  "unnecessary"  page
  faults.


And provides the precise definition in Section 3:


  We define  the  working  set  of  information  W(t,  r)  of  a 
  process  at  time  t  to  be  the  collection  of  information  referenced by  the  process  during  the  process  time  interval  (t - r,  t).
  
  Thus,  the  information  a  process  has  referenced  during 
  the  last  r  seconds  of  its  execution  constitutes  its  working 
  set  (Figure  2).


The term "page" in these definitions refers to physical pages, not virtual pages. That's because only those physical pages that have resided in main memory at least once during that period of time are part of the working set of a process.


  is the Working Set a completely different, separate list derived from
  the page table entries, or is it defined in the page table entries?


The working set is not defined by the page table entries. These entries define the whole virtual address space of the process. Also, by only looking at the page table entires, it's not possible to determine or derive the working set. The pages that are resident in main memory in a particular period of time and that have been accessed by the process in that period constitute the working set for that period.

Even if a page table entry includes an accessed bit (like the x86 page table entries) and even if the OS supports the accessed bits, it's still not possible to determine the working set just by looking at the page table entries. That's because the same page table entry may point to multiple physical pages during a period of time. At the end of that period, there is no way to determine all of the physical pages that any page table entry has defined during that period. So some additional data structures need to be used.