Got something that might work well for you! It's called Clear Gear Spray, you can find it at most Dick's sporting goods stores. I use it in my fishing waders, they get pretty stanky smelling from getting water in them and then taking a long time to dry out. They get worn a ton, often in very warm conditions, which as disgusting as it sounds, can create bacteria.
I got this Clear Gear stuff in a spray bottle, sprayed my waders very thoroughly inside and out and let them dry fully before wearing them again. The smell as gone, it smelled nice, basically like nothing, no nasty Febreeze-like masking effect. In the past I had tried washing them with light detergent in the washing machine (the recommended way) and it basically did nothing. I had also tried Febreeze which was only a very temporary solution. This shit is awesome and I fully endorse it. Apparently they use it for professional athletes (ie. hockey and football players) to clean pads and gear.
I gotta say I was extremely skeptical when I first heard about it but it's been about 6 months now and I haven't had to re-spray since!! Amazing.
Here's their website:
http://www.cleargearspray.com/ -- I got the 24oz bottle and I think it will last a very long time. If you were just using it on your boots 8oz would probably be plenty, its pretty cheap too. Just make sure you let it dry before using them, and take your liners out of the boot first.
