If you plan on accepting at least $3000 a month, PayPal becomes cheaper than Stripe. If you're going to be charging tens of thousands a month or more, then a merchant account with low interchange-plus pricing (that's a fixed markup over costs -- the interchange fees charged by Visa/MasterCard) is likely your best bet.
You can use Dwolla or Balanced, or work directly with a bank, to accept donations by ACH (bank transfer) as well. They cost 10-25 cents per transaction, which is much cheaper than credit card payments.
There is no issue of Payment Card Industry compliance when you're not accepting payment cards. That site provides an interface for ACH/bank-to-bank transfers.
You can use Dwolla or Balanced, or work directly with a bank, to accept donations by ACH (bank transfer) as well. They cost 10-25 cents per transaction, which is much cheaper than credit card payments.