There is a patch for Eclipse Neon:
https://bugs.eclipse.org/bugs/attachment.cgi?id=262418&action=edit
Download this patch and put it to the plugins directory of your Eclipse Neon installation. It will replace the default "org.eclipse.jst.server.tomcat.core_1.1.800.v201602282129.jar".
NOTE
After you add this patch you must choose "Apache Tomcat v9.0" when adding a server runtime environment in the Eclipse (Preferences > Server > Runtime Environments).
I.e. this patch allows you to select either Tomcat version 9.x or Tomcat version 8.5.x when adding Apache Tomcat v.9.0 runtime environment.
More details on can be found on the related bug report page: https://bugs.eclipse.org/bugs/show_bug.cgi?id=494936