I can only speak under UK tax rules, but you might find they are similar to your own.
Self employment can be tricky if you only work for one company, as you are not really generating your own employment (I think it was called IR35 restrictions and it caught many plumbers and electricians who said they were self employed but who worked solely for a house-building company, for example).
I run a limited company with one other person, and that company invoices the companies for whom I fly for my time as a pilot. This allows me to run a profit and loss account, including paying myself if need be. Any profit comes under corporation tax rules (10% on any profit), and any personal income tax as appropriate. The aircraft owners like it because they simply pay the gross invoice and there is no PAYE or other issues to be concerned with.