Freelancer here, I also ran my own cheap SaaS for time tracking / invoicing from around 2005 to 2010.

I've used Waveapps since I shut my own service down. It's pretty complete as an invoicing and report generator, free if you're not taking payments through them, reasonably priced if you are. I don't accept credit cards anyway, since as the OP pointed out, why would I want to give away 3% of my annual income?