For a freelancer starting out, any method is usually fine. When I was freelancing, I accepted Cash and Cheque, simply because I was not big enough in my first year to take a Credit Card while still making a profit. Company cheques are usually safe, but there will probably be a couple in your lifetime that bounce. The main thing is, you want a paper trail.
This can be accomplished even with cash, by issuing a receipt of course, but Credit Card processing, Cheques, PayPal, etc. will all have receipts and paper trails to go back on as well. In Canada, banks charge the least amount for depositing company cheques to small business/freelance workers; the rates for Visa can be between 6-9%, plus any extra bank or machine fees! This can easily turn out to be a lot of your profit, and should be taken into account. One trick to avoid some of these fees is to offer a discount if paying by cheque or cash, but do not increase the price for Visa or Mastercard; that is illegal in Canada.
In theory, it will depend though, again on the project size, and your fees for accepting payment. I do not have experience receiving money with Paypal though, so I would be unable to comment on that.