I tried to open putty ssh connection over SOCKS5 proxy via command line.
putty.exe -P port -pw password username@host -nc proxyhost:proxyport
This command doesn't work and I think it is incorrect. I tried a lot of variants of this command, but putty user manual doesn't contain necessary information.
I tried to connect to my host throw putty UI and it works fine.
For openSSH similar command looks
ssh -o "ProxyCommand=nc -x proxyhost:proxyport %h %p" -p port username@host
If I were you I would create a "Saved Session" with Putty and launch it via command line:
putty.exe -load session_name
It will be easier to create a "Saved Session" via the PuTTY interface than toying around with the command line. And it seems like you already have it working through the PuTTY interface.