Use your up smash on the hands to cause considerable damage. You do need to be skilled at dodging their attacks, of course.
Use your Aerial Down A on the hands. This can do more damage than the above method, but it requires a perfect hit. Otherwise, it gets slightly less damage, but still a good amount. It is also easier to jump out of the way of attacks with Yoshi.
Go for Crazy Hand first. Use up-tilt and take serious advantage of Falco's jumps and midair dodges. When Master Hand shoots the bullets at you, use your reflector, and when they do the lasers, use your gun or up-tilt.
This one is simple, yet incredibly tricky. it requires elite timing skills and a good sense of evasion. Use Counter on all their powerful attacks except the projectiles. Try not to miss a Counter, for it could be the last thing youm do.