Where should the line be drawn regarding political statements in a scientific report?
This appears to have been under the instruction of President Trump, as news sites reported data on the EPA website was removed.


Speculation usually doesn't belong in a scientific paper. This is especially true when it does not further the scientific purpose of the paper.

The rest of the statement - about the document no longer being available at its original link, and a note regarding its availability on archive.org, is fine because it is not speculation and serves an academic purpose. However, you actually don't need to resort to archive.org, because the document is still available on the archived state.gov site.

Like whitehouse.gov, the entire State Department website is routinely archived at the end of each administration, and the new administration can put whatever they want on their new site. (For example, at the beginning of the Obama administration, they replaced the Bush-era State Department site on climate change with their own.) The state.gov material from the Obama administration is still available; you just have to replace "www.state.gov" in the URL with "2009-2017.state.gov".

(P.S. an archive of the EPA website immediately before the transition, created in response to numerous FOIA requests, is also available: https://19january2017snapshot.epa.gov/)