Q-tip and I had this problem last year. She was so used to being out running during the day that she got really upset when I had to lock her up. Things to try:
Feed bunny right before you lock her up so she has something to do.
Spray with water bottle (Q says "ooh, fun....water!! Spray me again!)
Bitter apple spray on the bars (Q thinks it tastes YUMMY).
Hot sauce on the bars (Q says mmm, habanero!)
The only thing that worked for us even for a little bit (and only because Q was in her little cage, not the big NIC one) was for me to toss a towel over her the first time she rattled, and then after that, I'd move her to the bathroom. I would hold her off for a few days after the night in the bathroom, but she'd start again. When the nights in the bathroom didn't faze her anymore and she would just keep rattling, I sucked it up and let her be out during the night. Now she sleeps peacefully on the chair next to my bed all night long.