You can use whatever controller you prefer, so keyboard, gamepad etc. The idea is just to stay within the limits of an NES controller. So your game should only require the equivalent of a D-pad, Select, Start, B, and A. No extra buttons beyond that.
How you map those inputs is completely up to you. For example, I usually do something like:
D-pad -> Arrow Keys
Start -> Enter
Select -> Shift
A -> Z key
B -> X key