Keyboard shortcuts for new window in Chrome or iTerm2
To make a single hotkey always create a new Chrome window, launch Automator. Tell it to create a new Service Have the service take no input. Assign a single action to the service: Run AppleScript (in the Utilities list of actions).

Here is the AppleScript:

on run {input, parameters}
    tell application "Google Chrome"
        activate
        delay 0.1
        make new window
    end tell
    return input
end run


Save the service with a name like "New Chrome Window". Then, in System Preferences assign an unused keyboard shortcut to the service. You can then create a new Chrome window no matter what application you are in.

To improve the service substantially, replace "Google Chrome" with "Safari". :-)

To create a new window in a different scriptable app, replace "Google Chrome" with the name of the app you want to create a new window.