It might depend on the version of navigator you're using. I have V7R1M0
installed, working on IBM i systems that are all at V6R1.
Open navigator and locate the connection (system) of interest; expand it.
Expand Databases, then Schemas, then the schema containing the indexes
you want to delete. In the hierarchy pane click on Indexes under the
schema of interest, and all of the indexes in that schema will appear in
the objects pane. Select the ones you want to delete - you can select
ones that aren't adjacent in the list using the ctrl key plus the mouse
- and then right-click on one of the selected indexes and select Delete
(or, after selecting ones to delete, press your Delete key.) A
confirmation window with all of the indexes selected for deletion will
appear. If the list is correct, click on the Delete button in the
confirmation window.