Quote:
I tried creating a dummy variable, set to $true before the /whois, and set to $false in the raw. In the main code, I did a while loop to wait until the variable was $false. It never was. The code kept cycling until I broke it, and then the /whois showed.

This is due to mIRC scripting's single-threadedness, only one piece of code will be processed at any one time. This means that even if you got the /whois reply instantly the raw event would not be processed until it had finished with your alias. I should have been clearer about this before (not that it makes much difference, since in most cases lag will mean your alias is done before you recieve the server's reply in the first place).

You can't make an alias to return whether or not a random person is online. You can draw on mIRC's notify list as Online suggested, though you can't do something like this:
Code:
alias IsOnline {
  notify $1
  return $notify($1).ison
}

It will always return $false, unless they were on your notify list before (and mIRC thinks they're online).