Lanturn beats Substitutes with Waterfalls. I'm not quite sure if it can take on HP Grass or Ground Raikou by itself (it seems like Raikou could start setting up Calm Minds on weak Waterfalls before dealing a ton of damage), but it does beat HP Ice Raikou completely, and I think it also beats Shadow Ball Raikou. It can also Thunder Wave against non-Sub Raikou, which I think was the main point.
For Gallade, if it uses a non-Stone Edge move it breaks Subs 100% of the time. I don't think we can assume Raikou is at +1 and behind a Sub if we are interested in checking it. Otherwise Gallade is a solid check.
Any move not named Close Combat will fail to KO. That's why Gallade is probably going to have to use Close Combat if it wants to stop Raikou. Oh, and not to mention if it uses anything like Stone Edge with 8 PP it will run out of PP after 4 uses...
And Whistle, while I agree with most of your post, I have a couple issues. Your spread is pretty outdated, though it might not matter for some checks. I use 232 SpA / 24 SpD / 252 Spe and it's awesome.
How is Nidoking a check? Remember, most are Rash.
If Nidoking comes in after a Calm Mind, it is OHKOed:
493 Atk vs 167 Def & 303 HP (70 Base Power): 296 - 350 (97.69% - 115.51%)
If it comes in when Raikou has a Substitute up, it is 2HKOed:
329 Atk vs 167 Def & 303 HP (70 Base Power): 198 - 234 (65.35% - 77.23%)
If a Nidoking (with EQ, not Earth Power) comes in, somehow, with max HP, while Raikou is sub and CMless, then maybe it is an ok check, but you basically need to sacrifice it. I think that falls under your green definition.
And how is Electrode a counter? What can it do other than Taunt and die.
How is Alakazam a check? If it comes in after a Thunderbolt, it can't do anything really except Encore and lose half its HP.
How is Hitmontop a check? Raikou can just Substitute to block Close Combat and OHKO with Thunderbolt. Technitop doesn't do any better without using Close Combat (meaning it loses than and there). It doesn't 2HKO with Mach Punch:
317 Atk vs 186 Def & 321 HP (60 Base Power): 144 - 169 (44.86% - 52.65%)
and Raikou easily 2HKOes with Thunderbolt:
329 Atk vs 226 Def & 301 HP (95 Base Power): 150 - 177 (49.83% - 58.80%)
Regirock is not really a counter by any means, it can't switch into Calm Mind and take an attack because it doesn't KO:
328 Atk vs 186 Def & 321 HP (100 Base Power): 254 - 300 (79.13% - 93.46%)
and +1 Thunderbolt gets a clean 2HKO:
493 Atk vs 236 Def & 364 HP (95 Base Power): 213 - 252 (58.52% - 69.23%)
I gotta go for a bit, but this is a start....
Oh and, "lol" Shedinja.
EDIT: Lemmi, this is the same argument that was brought up last time Raikou was in UU. You can think of 100 billion Pokemon that can EV in max SpD and HP and maybe a bit in Attack and use a shitty Physical move, but in the long run that will hurt your team more than benefit it. Pokemon's standards are standard for a reason. They are better. Using your Stoss Ampharos is simply not viable versus every other Pokemon...