The short answer is - it depends. Depends on use cases, types of queries you are going to execute, document sizes etc.
I'd most probably have a document for each user, a document for each company, and then link between them using document references in one of them - with RavenDB its a simple string property that will hold the ID of the other document you are referencing.
The question is then - which document should reference which? User document to reference Company or the other way around?
This is where the answer is - it depends.
I have a post in my blog that discusses this to some length using a partial use case that you may find helpful: http://code972.com/blog/2013/12/610-many-to-many-relationships-and-ravendb-models