Expanding on my comment, the term stepmother is appropriate here. After all, it was Caitlyn's decision to become a woman*, and she appears to have adopted all the feminine terminology (for example, the pronoun "she"). Or, to be safe, you can refer to her as a stepparent. You could also just flip the entire thing and mention that Kim is Caitlyn's stepdaughter (as most tabloids seem to do).
I did find an article that uses "stepmother":
Reality TV star Kim Kardashian says that she first laid eyes on her stepmother Caitlyn, who was previously her father Bruce Jenner before undergoing a gender transition, when she attended the cover shoot of the magazine and she loved it.
Caitlyn Jenner is 'Beautiful', Says Step-Daughter Kim Kardashian
It's not unheard of to have two mothers (or fathers), especially when dealing with gay marriages. Even though sexual orientation is different than gender identity, they both legally fall under gay marriage laws.
It's important to mention that society tends to jump to heteronormal conclusions. This fact is illustrated by the experiences of a man with an ex-wife, who has married another man named Dean:
Indeed, there have been occasions in which Dean has been introduced as a “stepparent” by my children in public settings when their mother and I were around. The common assumption? That Dean was now married to their mom rather than in relationship with me, because stepparents are an accepted norm in a straight world, and still an oddity in the world of same-sex parents. This would both bring gales of laughter along with the sad recognition that we live in a world in which only children with straight couples who remarry can have stepparents, leaving the LGBTQ stepparents out in the dust.
The Complicated Role of a Same-Sex Stepparent
On the other hand, you can also witness the same ambiguity when you have a number of aunts and uncles: you don't know who's married and who's a sibling. There are social cues that help with this, but linguistically, we haven't solved the ambiguity. But we've managed so far.
* Caitlyn fits into the "stereotypical" image of transgenderism: her biological gender at birth was "wrong" and she was really the opposite gender. Of course, gender isn't always binary... Or constant, for that matter either (genderfluid).
In general, you should respect a person's preference for pronouns and other gender-specific language. Ideally, you would ask them (if they haven't already told you... Or Vanity Fair, in Caitlyn's case) what they prefer. There are a lot of different terms that may be used: here's a list of some.