I followed the steps on the fastboot quickstart guide, however the only difference is that I am using bootstrap-sass.
How do I tell fastboot that it should include jQuery?
It is explicitly not possible to use jQuery in FastBoot mode. For your use case, you might want to check out the ember-cli-bootstrap-sassy addon, which includes a recent change that skips the Bootstrap JavaScript imports in FastBoot mode (you'd need to pull the addon from GitHub, since this change has not been incorporated into a released version yet).
Related discussion:
As the FastBoot README warns: "Only the most brave should even consider deploying this to production." Hope you're taking that advice to heart =)