I would say
intuitively, but it feels like one of these situations where it might be ambiguous no matter how you respond.
However, if the dialogue was
A: Marie va venir ce soir?
B: Je ne crois pas.
Then I’d gravitate towards:
Moi non plus.
- meaning: "I don’t believe so either".
So, it looks like the response will refer to "je crois/je ne crois pas" more than to the "oui/non" that follows. Which makes sense: A says how she behaves, i.e. believing or not believing (that Marie will come).
In colloquial French, a simple reply stating an agreement avoiding the issue you have can be pareil or moi, pareil.:
– Marie va venir ce soir ?
– Je ne crois pas.
– Pareil !
In any case, both moi aussi and moi non plus will be understood as an agreement as moi aussi je crois que non and moi non plus je crois que non have the very same meaning.
To state a disagreement, the reply will likely use si or something similar, e.g.:
– Je crois qu’elle viendra, au contraire.
– Moi je crois que si.
– Moi, si !