I've just tried to link Google Stackdriver to the source code of one of my AppEngine projects stored on Github. The authorisation process goes well, but then I can't see the repository among those available to connect to.
Apparently I can see only repositories that belongs to "users" but not "organisations" on GitHub, even if I'm a member of that organisation (well... it's my organisation :D).
I couldn't find any help in the documentation.
We have to grant Stackdriver the access to each of the 'Organisation' we want to connect, by clicking the 'Grant access' button in front of each organisation name, in Github consent page, the first time you connected Github with Stackdriver.
In any case you missed to grant access there,
you can simply go to 'OAuth applications'(https://github.com/settings/connections/applications) section in Setting and select 'Google Stackdriver'. There you get the same screen where you can grant access to each organisation you like to share with Stackdriver. Once granted, all the repos under that organization would appear in your 'Select source from GitHub' dialog.