Use NodeAt to get the node you want to mess around with.
MapNavNode n = map.NodeAt<MapNavNode>(q, r);
You could for example set the Y in
MapNavNode.localPosition. Note that this is normally manipulated during grid creation time so it should be save to for your to make changes to locaPosition at runtime. Functions like
SmoothOut, and so on normally changes it. So if you do use these at runtime then it will be changed.
It might be best to work within your map's node height stepping and also to set "H" in node since that might be used by some other functions like OnNodeCostCallback which needs to know how high the node is in "steps" relative to other.
node.h = 2;
node.localPosition.y = node.h * map.nodeHeightStep;