When setting up a client with an eCommerce site, we typically suggest Paypal because they accept all the major credit cards. What's best is that they don't charge anything until you use them.
I have heard people complain about their rates, but if you want to jump through hoops to save 1/2% or something like that, then I think you're concentrating on the wrong areas of business.
Paypal did get a lot of 'bad press', but mostly from the eBay crowd. You know, people selling 'junk' and advertise it as 'new', then they complain when the purchaser want's his money back. That's not a Paypal issue... that's just stupid people trying rip people off.
Overall, I would suggest Paypal at least as a start. You can always change when you 'get your feet wet' with online payments and invoicing, etc.
Hope this helps! Good luck!