I was just in YYZ airport yesterday and the NEXUS office is located right next to the immigration hall entrance for US-bound flights in Pier H.
I walked in, put my name down on the "update" list and I was called 3 minutes later. There are two lists to put your name down for - appointments (must be scheduled in advance) and "updates".
The CBSA officer took my NEXUS card, four pictures of my eyes and then a fifth shot to confirm it could read my iris correctly and confirm it's me.
I then went through the immigration hall but because I think fingerprints are more easily read than irises I decided to use the GE machine. As always, worked like a champ.
-RM