First make sure that your local session is not capturing away the shortcuts from your remote session. I like using this trick: faq.i3wm.org/question/1679/toggle-i3s-listening-behavior/ on my local session but you can also use whatever method your vnc client provides (e.g. Remmina has a keyboard icon that when pressed will send all all keys directly to your remote session)
Then at the remote server make sure that xev reports key events when pressing and releasing the windows key. Run xev
from a terminal, make sure your mouse pointer rests on xev's window and hit the windows/super key. You should see something like this:
KeyPress event, serial 27, synthetic
NO, window 0x2000001,
root 0x25, subw 0x0, time 378034015, (-1,97), root:(515,117),
state 0x0, keycode 89 (keysym 0xffeb, Super_L), same_screen YES,
XLookupString gives 0 bytes:
XmbLookupString gives 0 bytes:
XFilterEvent returns: False
Take note of the description of the key next to its keysym: Super_L
in this case.
Next run xmodmap -pm
and look at the line starting with mod4. Next to mod4 it will print what ever key is bind to mod4. If everything is OK you should see this line among the output:
mod4 Super_L (0x59)
But since you're reading these lines it probably displays nothing next to mod4 or it displays some other key (e.g. Meta_L). To fix it run these two commands:
xmodmap -e "clear mod4" # un-bind mod4 from what ever other key
xmodmap -e "add Mod4 = Super_L" # <--- again replace Super_L with whatever xev gave you