I have the Whiteface '85 reissue and it's amazing. I bought one of the Rat 2 pedals before I got the '85 and it to was nice but the WF reissue is on another level. If you can find one or a vintage one, I would suggest those.
My favorite is my 87 first run RAT2 made by Woodcutter. It has a little more sizzle than my 86 black label small box. I have a 96 RAT2 that sounds really good too. My FAT RAT sounds identical to my 86 now that it has a vintage LM308N in it, but the ODPO7 chip sounds just fine in my other late 90s US RAT2.
The best RAT, as a connoisseur, is definitely the cheapest and closest to where you are stock RAT of any sort. Turbo RAT is different. You might like it tho!
In my experience, any of the Proco Rats WITHOUT an LED will sound better than any one with an LED. This may not be because of the presence of the LED, but it's a useful marker for a better-quality Rat in my experience. YMMV.
I’ve owned a few - the whiteface reissue is really special - I like it more than the vintage ones I’ve had. The old ones and the reissue all have noticeably better build quality, better feeling lots, etc.
So while “best” is subjective, that’s what I’d go with if looking for “best”.
Something about the old small box and the wfri where they are easier to dial in to whatever you want. It may be something as simple as pot taper, but that’s part of what made these ones stand out for me.
Sound wise, the new rat2s are quite close. They really nail the aggressive side of the rat, though I found it tricker to dial in some of the warmer sounds of the old ones. The mooer black secret comes really close to nailing those warmer rat tones, but feels a little more compressed and not quite as punchy.
IMO, the best RAT is also the best clone. The MXR Bass Distortion is a Fuzzrocious modded RAT with a Turbo mode and a clean blend. It sounds fantastic on both bass and guitar. I had a late 90s RAT and a GGG clone, and I kept the MXR. And now, as I'm considering selling nearly everything in favor of a Helix, I'm keeping the MXR until after I can compare it to the stock model.
My faves have been 90's Rat2, followed by the big box vintage reissue.
I have a Soothsayer now and like it a lot because it is very versatile.
I have used a few "clones" including the HArtman LM308 and Mr Vermin. They all do well, and I assume the props given to the very small and affordable Mooer Black Secret can be included. The down side I find with my Rat clone expereince is that it is more difficult to dial it into its sweetspots where all the controls mesh into a really great tone.
I feel you'd be safe trying any Rat you can get a hold of. Just don't be afraid to go all the way to each extreme on the gain and filter controls. Also, let the guitar controls do much of the tone shaping for you.
My favorite Rat versions are different from other players' faves. You really need to dig in with your own ears and own rig. I have found as much variation of the ProCo Rats of the same version as I have expereinced across diffferent eras and models.
I have three (4?) RATs: 88' black-face small box no led, R2DU which is the 80's rack & a modded White-face reissue. My favorite is the 88 although I use the WFRI the most and it's been modded by alchemy audio w/ an LED, Boss type power jack and a proper switch. I think that is the route to go (worked for me) if you can find the reissue fairly priced...
Best I had was a white face reissue, though the new Fat Rat is awesome and sounded pretty much identicle. I would also be completely happy with the off the shelf new ones for under $100. I doubt I would notice a difference if I wasn't hoarding a few at the time for spare backup boards and such.
The chip "upgrade" is a bit subtle to me.
I would start with any used one you can find. I had a Rat2 that was amazing as well.
Definitely my desert island boost to overdrive to fuzz in one box pedal.
You can get a big box, or small box for that matter, from the '90's quite a bit cheaper than the WFRI, and they sound awesome. I have had a ton of RATs and my keeper is an '86 small box, but I have had a bunch from the early 90's that sounded awesome. On the cheap, the Mooer Black Secret is very close to my '86, and it has a Turbo mode built in.