Brake caliper replacement rubber tip goes in top or bottom hole?

The picture shows the rubber on the top pin at the end. It goes on the leading pin, or the one the rotor hits first as turning.

Correct. You should have a rubber boot on both the top and bottom caliper pins. This is to keep dirt and brake pad dust out of the pin so that the caliper can slide easily.

Here is a guide that talks about this as well. Let us know if you have other questions. Thanks

https://www.2carpros.com/articles/brake-caliper-replacement