The only two tourist areas in Nicaragua that I know that have kayak tours are Granada and the island Ometepe.
There was a tour promoter doing kayak tours of Lago Apanas in Jinotega that may still be around. There was only one tour operator that advertised river rafting in Matagalpa on the Tuma river. It mainly comes down to if you want to explore independently you will have to bring your own equipment.
(Guatuzos Wildlife Refuge, Nicaragua, pictured.)