Phrase choice for "one of x preferred colours" when two colour choices are equivalent
The strongest statement you can make in this situation is that green is one of her three most preferred colours, as saying that it is one of her two most preferred colours implies that there are two colours preferred to all others.
We usually speak of a person's favourite colour or colours. Prefer implies a choice between two things (or a small number).
Green is one of her three favourite colours, but she prefers red.