Plan to get car in Pisa at airport and from there later take train to Milan, what charges would we we encounter for drop off?
The website of your rental agency will tell you if there is an additional fee for picking up at that airport (or dropping off). Since you are picking and dropping at the same place there shouldn't be any additional charge.
Picking up and dropping off both in Pisa? No drop off charge. There's usually not even an airport premium in Italy. Where you to drive to Milan, the cost would go up, not especially because of the second place drop-off, but because you'd have to rent from an outfit that had cars on both places.