tools: fix GYP ninja generator for Python 3

PR-URL: https://github.com/nodejs/node/pull/29416


Reviewed-By: Christian Clauss <cclauss@me.com>
Reviewed-By: Rich Trott <rtrott@gmail.com>
Reviewed-By: Ujjwal Sharma <usharma1998@gmail.com>
Reviewed-By: Ben Noordhuis <info@bnoordhuis.nl>