But for instance if there are 2 bodies different size but moving in same direcion SAME velocity and if you apply force from the side the one which has large momentum(due to its weight)will get deflected from its path less than the one one with small momentum(due to less weight). If this is the case then why cant we apply it to our aircraft.
What you are saying is true, however if the wind is stable, you've already adjusted for that, and that's one reason size and weight are not factors. In the case of gusting winds, yes, the change in wind speed effects a force on the aircraft, for which momentum (related to 'weight' - actually mass, but for this discussion weight is OK) would affect the amount of movement.
Also to be considered is the 'shape' of the aircraft... a large tail could cause the plane to 'point' into the wind, a large front end could cause it to point away from the wind, an airplane with the nose wheel on the ground will be less likely to point into the wind than one with the nose off the ground or a tailwheel airplane... a high-lift wing could cause the plane to be affected more than a low-lift/high-speed wing
So yes, you are right, to a degree, however the shape of the plane, wing, and tail, wheel configuration, position at the time, speed, variance of the wind, and many other factors have effect on how much a crosswind will affect an aircraft. These other factors generally have greater effect than mass (weight) and size.
Generally, a 'big' airplane (think A380 or 747) will be less affected than a 'small' airplane (think Cessna 152), however to give an example where shape is more of a factor, think of the space shuttle versus an A380. The space shuttle has almost no lift compared to the A380, and thus the A380 is more affected by cross wind than the space shuttle, but the space shuttle is about 1/4th the size and mass (weight) of an A380.