The best way to see the most of the islands in comfort is aboard the small cruise ship Africa Princess. Week-long island-hopping trips run from CFA700,000.
Otherwise, travel between the islands can by trying. Rubane is easily reached; Canhabaque slightly less so. Transport to other more remote islands can be expensive and unpredictable – the high-end resorts and Orango Parque Hotel all offer boat trips for guests. The schedule for public canoas is challenging to discern to say the least.
It might be worthwhile to contact IBAP in Bissau to see if they have a team of researchers in the islands. It's possible you could join them on a leg of the journey if they have space.