I'm going to assume that you mean you want to send SSH commands without have to use the Putty GUI running on Windows. There is a command line version of Putty called PLink. There are only precompiled binaries for Windows, but it looks like you can make your own Linux-compatible ones (can run on cRIO) from source:
https://www.chiark.greenend.org.uk/~sgtatham/putty/faq.html#faq-unix
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A.3.2 Is there a port to Unix?
There are Unix ports of most of the traditional PuTTY tools, and also one entirely new application.
If you look at the source release, you should find a unix subdirectory. You need cmake to build it; see the file README in the source distribution. This should build you:
-Unix ports of PuTTY, Plink, PSCP, and PSFTP, which work pretty much the same as their Windows counterparts;
-Command-line versions of PuTTYgen and Pageant, whose user interface is quite different to the Windows GUI versions;
-pterm - an xterm-type program which supports the same terminal emulation as PuTTY.
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You should be able to call the Plink binary on the cRIO itself using the System Exec.vi. The commands you are currently running from Putty should be pretty similar when executing them using PLink.
If you don't want to deal with compiling your own PLink, it looks like there are other options like OpenSSH. It looks to be available on some of NI's feeds as an .ipk.
http://download.ni.com/#ni-linux-rt/feeds/2018.5/x64/core2-64/
Here is the direct link since the NI website devs have made the feeds unnavigable. If your cRIO has an internet connection, it will be easy to install. If not, it will be a nightmare if it has many dependencies.
http://download.ni.com/ni-linux-rt/feeds/2018.5/x64/core2-64/openssh_7.4p1-r0.5.83_core2-64.ipk
