I currently have a google checkout account, would this work well or is their something that is a lot better?
Checks are great because you get to keep all the money...well, except for taxes later,
Wire Transfer (Bank) is a great option if the invoice is huge (more than $3000), to avoid costly fees.
The other options suggested above are good alternatives, too.
You can send a bill (including recurring bills) to clients, and have a full list of all invoices and whether they've been paid or not. They can pay with a credit card or bank account, and then you can either direct deposit the money into your bank account, or send yourself a check for the money.
For online payments, Google Checkout should work fine unless you have any particular gripes with it.