Mega Gengar is really strong. I can see why one would argue that. It just fills a similar role to Zam, which is absolutely ridiculous in this meta. That being said, let's keep it in perspective that it is much easier than Eevee to use, due to having great offensive stats. You could basically just smack things with it and still do alright. If there is any reason to use Eevee, it is the fact that so much relies on Rest for recovery/status removal. Even if it's being used sub-optimally, that makes it very strong. Support mons can definitely be just as strong, or even stronger than dominating offensive mons.
It has some pretty notable distinctions over M-Alakazam. I'll list some from the top of my head:
1) The ability to use Will-O-Wisp to cripple A-Muk, or Protect + Disable to overcome it. Both of these strategies allow it to eventually 1v1 A-Muk. M-Alakazam is hopeless against A-Muk.
2) Ability to 2HKO Melmetal, a premier Pokemon in the metagame. With M-Alakazam, Melmetal can usually switch in once or twice (dependent on whether your opponent uses Psychic or Shadow Ball on switch in) and threaten the OHKO in return.
3) The existence of Will-O-Wisp is also a nice mid-ground play, and really eases prediction when the opponent is carrying one of A-Muk, Snorlax, and Melmetal (99% of teams will have at least one of these).
4) The Ghost typing is also a neat perk, as with Taunt, it can overcome Chansey. With M-Alakazam, Chansey can still win out with Seismic Toss.
5) Superior STAB moves as Ghost + Poison > mono Psychic.
Just looking at all the available Pokemon, there really isn't a true, reliable counter to M-Gengar. This fact alone warrants a rank higher than B, at the least. Also, the type differences between the two of them (Gengar and Alakazam) only distinguishes them further.
I do agree that overall they share similar roles in being fast, powerful cleaners, but I just wanted to make the point that M-Alakazam doesn't straight up outclass M-Gengar. M-Alakazam's advantages over M-Gengar are Calm Mind and a faster Speed, but I don't think is enough to outright state it's simply superior to M-Gengar. In my opinion, they should both be ranked together in S.
As for Eevee, Ryolain already covered my response, but I'd like to reinforce that being the only cleric in the tier doesn't automatically warrant an S rank (which it previously was, which I found absolutely ridiculous btw), nor an A rank. Personally, an upper B rank is fair for me. I say this because, again, it really isn't an effective cleric, and very often has to sacrifice itself just to do so.
TL;DR - M-Gengar has enough distinctions from M-Alakazam to be ranked independently of it (as in, the existence of M-Alakazam shouldn't deduce the viability of M-Gengar).