I think your analysis is good. NIR is passing through all three Bayer filters (even the green channel has light foliage). So there is not a very good visible-light only channel. I don't see how option 3 above (a filter to clean the blue channel) could work. NIR is passing through all Bayer filters and seriously contaminating all channels. You can't add a filter that blocks most of the NIR (you just removed one of those). If you add a filter that blocks some NIR, maybe the green channel would see mostly visible light and another channel would see mostly NIR. But it seems like a stretch.

Channel math might be the only option with this camera, but I never quite understood how that works.

Re: option 3, i was half-heartedly thinking of making a second Bayer filter by photographing a checkerboard on film and printing lots of negatives, but it's really a bad idea, since you'd have to line it up quite well with the existing bayer filter upon installation, which is totally impractical.

The idea of using green for visible light isn't nearly as good as blue or red... but Chris is right, the green channel doesn't seem to leak as much NIR, so I thought a little more about it.

Look at this image, from the old near-infrared-camera page (maybe we should resuscitate it, the graph is quite useful):

The green is certainly not as absorbed (the example is a graph of eucalyptus leaf absorption i found somewhere) but it is pretty close to red/blue, when you compare it to infrared. Granted, the sensor itself may be less sensitive to infrared -- so the graph we'd see of what the sensor actually detects may not be as differentiated. But green still seems to be quite correlated with photosynthetic absorption, and could still be quite useful.

See the diff between R and G channels, above -- although it's rather "grungy" data since the dynamic range wasn't good, but with more rigorous testing, perhaps it is useful... what would be the next step, testing this technique against the Canon NDVIs?

Is there any thought or possibility to make this camera active rather than passive?

From what I understand (which is not much, I'm pretty new to this) and have found online is that for some reason, CMOS cameras produce results that are not nearly as good as CCD digital cameras.

You can check out this site page which shows a few comparisons between CMOS and CCD cameras.
http://flightriot.com/category/vegetation-management/

Yeah, that guy's been on the infrared mailing list a lot recently (http://publiclab.org/wiki/mailing-lists) and it's great to see his results. Still, I've seen some webcams (presumably CMOS) which do very well, like Stewart's --

http://publiclab.org/notes/gonzoearth/06-20-2013/rocketfish-hd-webcam-conversion

http://publiclab.org/notes/gonzoearth/07-02-2013/infrablue-webcam-panoramas-in-the-oakland-hills

I'm still trying to figure out what the difference is.

Perhaps the exposure settings play a big part as well. Brenden at flightriot.com and myself (mostly him) have been experimenting with different camera settings. I am very new to this all and still learning but it seems that the White Balance settings play a huge role in the overall quality. Obviously the LUT is customizable and I believe that the processing end (imageJ/Fiji, ned horning plugin, etc.) are pretty straight forward (basically some addition/subtraction) so it has to be the exposure settings...right?

Well, definitely WB is an element, but what seems to be the big thing is that on these cheaper cameras (with the exception of the one Stewart tested) the blue channel detects infrared light -- which is not true on the CCD and more expensive CMOS cameras we've modified.

Is that something that could be corrected with a specific filter or an inherent issue with the quality of the camera?

My best hypothesis right now is that it's related to the Bayer filter in the camera itself, so I'm hoping to order more different cameras and find one that works.