I’m certainly no expert on this type of thing, but I’ll attempt to answer.
As far as I know, they portion that allows you to hook into the EndNote plugin API must be written in (unmanaged?) C++. Additionally, I believe you must implement any callbacks and call any EndNote API functions in C++.
However, you can write your own functionality in any of the .NET languages and call these from the plugin code written in C++. (and of course, you can also call managed C++) That’s basically what I did a while back. I wrote a library in C# and used it from both EndNote and a Word plugin.
Hopefully someone can correct me if I’m wrong.