Does the material of a ball affect how high it goes when you throw it up in the air?

The material of the ball does not affect the height it reaches when it is thrown up. The equations that describe the height which reaches a body when it is thrown vertically upwards are the following:

h = h0 + v0t + (gt^2)/2

h = (v^2 – v0^2)/2g

h0,  is the initial height, when it exists.

v0,  is the initial speed of the body.

g,  is the acceleration of gravity.

t,  is the time.

Balls made of different materials have different masses, but in the previous equations we can see that the height does not depend on the mass of the body. The height depends only on the initial speed of the ball and is independent of its mass, so that the material does not affect the height that it reaches. 

So, when two balls of different materials are thrown upwards with the same initial speed, they arrive at the same height.