Dear Cesar,
you should either use the versions included in the tar file releases from sourceforge [1] or use the tip versions from bitbucket.
There was a binary-reform included in 4.99.19 (provide explicit arguments instead of guessing). From the error message you provided, on can see that the version of letsencrypt you are using assumes a version of NaviServer supporting the "-binary" flag. So either downgrade letsencrypt or upgrade naviserver.
[1] https://sourceforge.net/projects/naviserver/files/naviserver/
