I use sourcegraph[0] for most of my searches even on non-entreprise github to work around how broken github search is. Sourcegraph has the ability to search in forks, in a specific commit, or in a set of repos that you define. It's really quite good at doing github-wide searches of arbitrary query. I'm pretty sure its self-hosted solution can be made to work with github entreprise, you might want to check it out :).

Disclaimer: Just a happy sourcegraph user.

[0]: https://sourcegraph.com