In my opinion, Bako National Park is one of the most beautiful national parks I have ever seen. It is easy to reach from Kuching and because of the small size (it is one of the smallest national parks in Borneo) you get to see a lot of wildlife. You can either go for a day trip to the park or stay a night in the basic chalets.
Sipadan, a tiny island on the east coast of Borneo is rated as one of the best dive spots in the world. We were there to see it with our own eyes and yes, diving at Sipadan is incredibly beautiful! Read in this post about the dive sites, where to stay and how to get to these incredible dive spots.
Kuching, the capital of Sarawak, the biggest state in Malaysian Borneo, is a perfect base to explore the relativly nearby national parks. Besides that, Kuching is for most of the travellers the starting point of their Borneo adventure as Air Asia, Malaysia Airlines and Malindo Air have frequent flights to Kuching.