Thermal/LWIR nerd here. LWIR can't see through windows/glass. It'll show up as a gray blob and you'll actually end up seeing yourself because the glass reflects LWIR like a mirror.
50-100 yards to see a rabbit you'll need a good scope. Something that has a thermal resolution of 320x240 or greater or you'll just see a heat blob show up. Also bear in mind that many animals are insulated so you may not end up with an image that you expect. A strong thermal contrast will work to your advantage so on a cool crisp night you should be able to see better with more clarity. The greater the thermal contrast the better the image.
You won't be able to put the monocular in front of the scope for the reasons stated above with regard to glass. So like you indicated, it'll make a good spotting scope. You'll need something with a Tau core not a Lepton because the thermal resolution isn't high enough.
Let me be honest here -- you're looking at about $1500-$4000 to do what you want to do. LWIR gear isn't cheap. I've got a Lepton 3 (160x120) and had a Lepton 2 (80x60). At 160x120 at ~50-100 yards a human will look like a heat blob and that's a large human versus a small rabbit. 640x512 would be ideal for your use case and FLIR makes them in the Boson cores. They run about $4000.
I'd recommend NVGs over thermal for what you're doing but that's expensive as well BUT you can look through your scope with them. You'll see about 50% as bright through the scope depending on the size of the objective lens. I own a PVS-14 Gen3+ autogated filmless with a L3 Warrior Systems tube. You can probably score some Gen 2 gear or blemished tubes for $1500 or less.
Also realize any of the FLIR gear that's above 9Hz refresh rate will be considered ITAR equipment, much like the PVS-14. If you're ok doing *active* versus passive get you an IR spotlight and a camera that can see IR. Much cheaper.
Good luck and hope this helped.
