What indexes would I create for a query like this?
I would suggest the following two indexes:

charges(balance_id, refunded, invoice)
balance_transactions(account_id, type, created, source, fee)


The first is a covering index for charges.  The index should be used for the query with no need for the data tables.

The second is a covering index for balance_transactions.  The first three will satisfy the where clause.  The four column will be used for the join and the final is needed for the select.