Payment to contractor $1,000 (with payment app).

Payment to contractor $2,000 (with credit card).

Is $1,000 or $3,000 the correct amount to report on the 1099-NEC?

(The contractor, a competent bookkeeper, advised the client that $1,000 is the correct amount.)

Instructions: Form 1099-K.   Payments made with a credit card or payment card and certain other types of payments, including third-party network transactions, must be reported on Form 1099-K by the payment settlement entity under section 6050W and are not subject to reporting on Form 1099-MISC. 

So the instructions say 1099-MISC and don't mention 1099-NEC. If correct, and NEC is intentionally not listed here, then the total payments must be reported. 

P.S. These nagging questions remind me to avoid extending my services outside my tax preparation/tax consulting nice.