The IRS offers a quick and easy way to make your quarterly estimated tax payments online using their Direct Pay tool:

Taxpayers can make a variety of tax federal payments via this IRS on-line payment tool, such as tax return balances due, estimated tax payments, tax balances owed as a result of an IRS tax notice received, and installment agreement payments among other types of tax payments needing to be paid to the IRS.  Taxpayers using this payment site will receive immediate confirmation of the payment made using this website once the on-line transaction has been completed.

And most states offer a similar on-line payment tool as well.