This really depends on whether you already have a business checking account. Most banks partner with Authorize.net for online merchant services. If you do have a bank account contact your bank and they will be able to get you a better transaction rate than you could on your own going through Authorize.net. However, if you don't have a checking account then it depends on what level of integration you need with your online service. PayPal Payments Pro has some of the best integrations, consumer trust, and ease of use.

This is a hard question to answer without knowing exactly what application your merchant service would be interfacing with and what you would need it to do. If you want to discuss your project in further detail I would be happy to help you.