Of the two, it's normally command timeout you want to increase. There are certainly times when increasing it is the right thing to do, but do change with caution. If you set the timeout high, potentially your query will block others for that much longer. Ideally you want to tune the query first to get the time below 30 secs. I say 30 secs because that IS the default, so if you run queries longer you risk breaking other stuff (due to blocking) that doesn't have the advantage of a longer timeout.
Andy