My '96 Civic passenger window was broken and ever since the replacement of it (non-dealer), whenever I drive over 55/60 MPH I can hear a hissing/whistle through the window.

Note: The amount of hissing is dependent on how much air is flowing out of the car. ie. when all the windows are closed, the hissing is much more apparent and begins to be heard at lower speeds, when I open the sunroof or crack the driver side window a little, the hiss goes away. Obviously there is something about the airflow in and out of the car that has to do with it.

Somewhere there is air seeping in, I just don't know where exactly. I asked the dealership and they said I need a new 'run channel' and that it would cost over $100 to replace it.

Where can I buy one and is it easy enough to install (DIY)?

 

Yes, it's a DIY job. You need to remove the door panel (see service manual at link in my signature) to access the window channels. You may also need to replace the rubber weather strip where the closed window rests at the top of the door.

Check here for prices:

http://www.hondaautomotiveparts.com/

 

Check that the window is straight by opening it slightly. It should have the same gap from the glass to the frame all the way across the top (use the driver's window for comparison). If not it may just need to be adjusted. The shop that replaced it should do that for you under warranty.