I'm running a Hendrix Woodstock Strat into a Marshall JTM30, through a Dunlop Fuzz Face and a Vox Wah, directly into the amp's input. My question: Will I get effective noise reduction if I just put the Decimator at the end of the Fuzz and Wah, directly into the input, or should I put the Decimator in the effects loop? I get insane amounts of noise at higher volumes, so the Decimator seemed like the best option, but I'm confused about how it works, and where it goes in your chain?
depends where the noise is coming from. if its coming from a pedal or ur pickups, at the end of the chain will be fine. if its coming from the preamp, the loop.

what kind of noise are u getting? while ur playing or while ur stopped?
Mesa F-30 - 1x12 V30
PRS SE Custom 24 (GFS Crunchy PATs)
PRS SE Singlecut (Evo/Air Norton)
1989 Starforce (GFS PowerRails)
Morley Tremonti Power Wah, TS7 (808-Mod), Pitchblack, Boss DD-3, DE FnC
it should be the first thing if the noise is coming from ur guitar or just before the amp input if its ur effects causing the noise. experiment....

putting it in the fx loop wont accomplish much
It is like the second guy said. I watched a video on this because I still didn't understand how to do it but sometimes it is unavoidable. I didn't ever want to have to use a noise gate type device but well I had to. Some people use one right before the input and then at the end of the effects loop also. That would be the best way to eliminate all the noise but you suffer some tone control loss depending on the noise gate. Good luck!