There's generally no direct way of accessing a different-origin window object. If you want to securely communicate between content scripts in different frames, you have to send a message to the background page which in turn sends the message back to the tab.
Here is an example:
Part of manifest.json:
"background": {"scripts":["bg.js"]},
"content_scripts": [
    {"js": ["main.js"], "matches": ["<all_urls>"]},
    {"js": ["sub.js"], "matches": ["<all_urls>"], "all_frames":true}
]
main.js:
var isTop = true;
chrome.runtime.onMessage.addListener(function(details) {
    alert('Message from frame: ' + details.data);
});
sub.js:
if (!window.isTop) { // true  or  undefined
    // do something...
    var data = 'test';
    // Send message to top frame, for example:
    chrome.runtime.sendMessage({sendBack:true, data:data});
}
Background script 'bg.js':
chrome.runtime.onMessage.addListener(function(message, sender) {
    if (message.sendBack) {
        chrome.tabs.sendMessage(sender.tab.id, message.data);
    }
});
An alternative method is to use chrome.tabs.executeScript in bg.js to trigger a function in the main content script.
Relevant documentation