Hi, Gemnasium founder here.
Let me clarify things a bit :)
Gemnasium is a paid service for private projects only, and security notifications. It's free for opensource projects.
If you don't want to share your github repo with us (and I completely understand that), you can push your files to our API using http requests, or directly our CLI : https//github.com/gemnasium/toolbelt
Modern projects use more than one package manager (ie: bower or npm + something else). You don't need to mix tools with gemnasium, we support projects with multiple deps type.
Feel free to contact me if you have any question!