independent contractor working in US not through an agency

I am a Canadian living in Vancouver. My profession is Integrated Circuit (IC) design and verification engineer. I am in discussion with a California-based company to go there and work for them as a contractor for 3 months.

I thought that TN visa would allow this kind of arrangement. But the hiring manager just told me that their HR says that they will have to find a third-party Canadian-based agency and hire me through the agency instead of dealing directly with me. This is very disappointing for me as it means that the agency will take a big chunk of my pay.

Would a TN visa actually allow a Canadian independent contractor working directly for a company (not through an agency)?

Thanks for any feedback.