Discuss the pros and cons in this thread, hopefully it will help other make a good decision on what option to go with. I prefer online payment as it is quicker, although the fees are high. Checks can be sluggish as it can take weeks to receive (if no express delivery option is available) and weeks to be processed by the banks. It can be less expensive though depending on your bank.
Are you talking about payment through Paypal or payment gateways. Most have a chargeback. A cheque from a reliable company is always better
The pros usually with the check is that once you have the money, you have the money, unlike with credit cards - the merchant is subject to chargebacks. The cons with the check is that it takes time to get the check, you have to go to the bank, deposit it etc. Even if you accept checks online, you still have to wait for the check to clear, it is not immediate