It can rain quite a lot, usually in the afternoon and at night, and be windy with big waves. Occassionally it might rain all day. That being said, I also recall beautiful sunny weather with light breezes and no waves around new year. So, like the weather tends to be, it is unpredictable. It is quite hot and very humid.
You should be aware that the risk of malaria is higher in the wet season, and the Gilis do have malaria mosquitos, so it is essential you take malarial medication if you are staying there that time of year.
It is possible it would be drier around Kuta Lombok, so perhaps - if rain is a big concern - you should consider it as an alternative to the Gilis.