The quality of the mic will also play a major part in what it sounds like. Distance is one variable factor as are the plugs used..... but the mic itself is the most important part.
As I mentioned, the fact that you have 2 sound cards working in the single DAW computer is also playing into this issue. clicks, pops, latency, clock sync issues.....
Using a single external USB based interface, running ASIO (native....not wrappers and codecs) and using a decent condenser mic with phantom power will very likely solve all of the issues. (99.9999% chance) And a quality condenser mic will give you exactly what you are putting in to it.
Just about everyone here has made that move to an external interface. M-Audio, Presonus, Focusrite are good ones.... but not the only ones.... be sure they use NATIVE ASIO and have the other features you need..... and please avoid the ones that are 2 or three things in one..... guitar simulators, mixers, etc combined with an interface..... some are OK...some are not.
There's a difference between the breath pops that a pop filter tends to solve verses the pops and clicks introduced into the audio stream by mismatched soundcards and substandard drivers like MME. Neither are wanted in the music.