I am trying to find near field mutual coupling affects between two antennas - one being transmitter and other being receiver. The receing antenna is fed with very little voltage (I think, if I don't feed any source, then nec tool inserts default source). The problem I see is that nec tool does not show input impedance of individual antennas. Both antennas are kept half-wave length apart.
I think you have not clearly formulated your question. You write that you are, "...trying to find near field mutual coupling," but I suspect that you actually want to know the amount of current / voltage / power induced in a second antenna when you drive a first antenna with a specified amount of voltage / current / power.
This is available directly from 4NEC2 by driving the first antenna as specified and observing the current in the second antenna (which does not include a source). You can simulate the load impedance attached to the second antenna by placing a load in the second antenna's appropriate segment. Naturally, the power in the load is Z*I^2.
"It seems that what you need to do is to model each separately then together."
Yes... and... the quantity you want to measure is the mutual impedance. Mutual impedances between elements are measured by measuring the impedance of any driven element with other elements open- or short-circuited. These values are then combined to calculate the driving-point impedance of each element given its specified current and phase.
This is clearly described in chapter 11 of the ARRL's Low Band DXing by John Devoldere, ON4UN.
It seems that what you need to do is to model each separately then together. Do NOT model the receive antenna with any feed when modeling them together. You can compare the single antennas to the pair to see the coupling effects on the transmitting antenna. You can then do them together with the receive antenna fed and compare that to the single receive antenna again to see the effects.