We use intuit gopayment and square. Gopayment is our go to. They deposit the entire amount of the sale and then withdraw their charge which makes accounting (bookkeeping) much easier. Then you have a full payment to apply and a separate cc expense. Square deposits the amount minus the fees so when you apply payments, they are always short. For this reason, I hate square and wouldnt use it if I didnt have to.
Whats wrong with paypal? From what i read they have some of the best rates. We take it too and never had any issues.