What tools can help me determine if a plant homologous protein interacts with an ncRNA in the same way?
The ncRNA sequence from human may bind to the plant protein in the plant cells, but so what? You may be able to say the plant protein works as RNA binding protein, but no more than that.
Another concern is that the plant protein may not recognize the same RNA sequence to the human protein.

There are several ways to find RNA partners of RNA binding proteins.

SELEX

This method is used to find consensus sequences that your protein recognizes in vitro. Once you find consensus sequences, you can search ncRNAs from the plant.

CLIP

This is similar to Chip assay. You could find real targets of your RNA binding proteins