The forms I generally hear (or see written, in on-line communication), in order from most-common to least-common, are
Do you have a PayPal account?
Do you have an account with PayPal?
Do you have an account on PayPal? (this only occurs with on-line establishments, never with ‘brick-and-mortar’ establishments)
Do you have an account for PayPal?
I do not ever recall encountering ...account in PayPal?, and ...account at PayPal? only occurs, in my experience, when PayPal is replaced with a ‘brick-and-mortar’ establishment (e.g., a retailer or bank).