Ctrl-N in emacs keybindings for Jupyter notebook in Chrome
You can do this with AutoControl Shortcut Manager by using the SYNTHESIZE INPUT action to send a synthetic Ctrl+N from the inside of the webpage.
That way, the webpage will respond to the shortcut but not the browser.
This is how you do it: 
Set Ctrl+N as the trigger
Choose SYNTHESIZE INPUT as the action and enter the keystroke Ctrl+N
Select option Send from the inside of webpage
Now, whenever you press Ctrl+N, Chrome will do nothing, but the webpage will receive the keystroke and will react to it.
Of course, you'd only want to do this on those Jupyter Notebook pages, so make sure you add a URL condition to that trigger.