I've used Braintree for about a year in a mid-sized ecommerce situation. Not a single complaint to be had. I find the API very easy to work with, and the support to be very responsive. They have a nice drop-in payment form with built-in support for PayPal.

On the surface level, Stripe seems to offer more in the way of open source and integrations (POS, Analytics, etc..https://stripe.com/docs/integrations)