Square is great for that. It lets you customize your emails, logo, charge id claim, etc. I used that both as client and provider.

Stripe is amazing for an ecommerce platform, but i find some programmers not able to implement API right half the time...

You can learn it however through one month http://mbsy.co/c6bPT

Hope it helps

If you're just looking for invoicing, Freshbooks is great. Xero is another, but that's a little more of a full accounting system so that might be more than you need.

For B-B oriented small businesses or those that sell complex products and / or services for which you need to create proposals or estimates, track billable hours, or keep track of deductions based on a retainer:

Harvest App: simple and easy to use yet quite flexible (works directly with Stripe and Paypal).

17hats: way more than invoicing so could be overkill but definitely worth a look—you may not know what you are missing.

Freshbooks: also more than invoicing; especially good if you want WordPress integration via Gravity Forms, whereby you can turn an intake form into a configurable product or service invoice directly in Freshbooks—a nice time saver which also eliminates errors in transcribing.

As mentioned Xero is probably the best accounting package you can use which includes invoicing, however there is a great simple invoicing app called invoice2go - very cool
http://www.invoice2go.com

I recommend FreshBooks.com too. So far it seems to be the easiest to understand and use.

Most of my businesses utilize Freshbooks and then convert to Quickbooks Online when they have established a cadence. Freshbooks is a nice place to start because it's cheaper and easy to use and then when you end up getting more deal flow you can change over to QBO for a more advanced integration between bookkeeping and AR. This approach allows you to get inbound revenue easily and in an automated fashion while you construct your chart of accounts and then can switch over to "real" accounting.