Hi Red Mystic,
I have had the same trouble as you. This census in particular is frustrating because it does not record the place of residence, only "Country or Province of Birth." After looking through each page of the census for District No. 2 New Westminster, Sub-district Coast C, Division 33, here is what I found. The Queen Charlotte Islands are listed on pages 47-77 of the above section (out of 185 pages in all). Although the listings do not specify where each individual was enumerated, one can assume that Rowland Green (the enumerator for QCI) didn't ask where each individual was born, but assumed that the people he found in each village were from there (of course, this is only a guess).
The aboriginal population of QCI starts on line 11 of page 47 as denoted by (Ind) next to the name. The place of birth is entered simply as "Q.C. Islands, BC." At the top of each of the following pages up to p.77, the first name on each page also has (Ind) noted with a ditto mark (") beside subsequent names.
"Masset, Q.C. Islands" is noted to be the birthplace of those aboriginal peoples listed on p.57. Unfortunately, p.58 lists only "Q.C. Islands" as the birthplace again, until near the bottom of p.59, where the birthplace is changed to "Kauing."* This birthplace [Kauing] continues for those aboriginal peoples listed to the end of p.60. Page 61-62 again lists "Masset, Q.C. Islds" as the birthplace. Most of the names on pp.63-64 list "Gold Harbor" as their birthplace, and then from pp.65-73, "Skidegate, Q.C. Isds" is listed as the birthplace for most of the names (with a few Europeans and a family from Kitwanga interspersed). Near the bottom of p.73, and continuing to the middle of p.77, "Clew, QC Islds" and then, "Clew, B.C." are listed as the birthplace. Thereafter, Japan and China are noted as the birthplace for many pages, signalling the end of the enumeration of the Queen Charlotte Islands.
I hope this is of some help, if a bit late. I only stumbled upon your post today and thought I would share what I found with you in case you are still interested in this question.
*I thought this might be the village, Kung. However, this village was only occupied from about 1853-1875 (according to Kathleen Dalzell. 1973. The Queen Charlotte Islands: Places and Names. Volume 2. Madeira Park: Harbour Publishing). If this is the village that was meant, then perhaps Green did ask people's places of birth because Kung was likely unoccupied in 1891, but it is very conceivable that many of the people enumerated in 1891 were born there in previous decades ...