Fast answer
A no-car Menaggio arrival should be planned as a sequence, not as a single destination pin. The Como bus route can be direct for the western shore, while a Varenna rail-plus-ferry arrival can make sense when Milan train access matters. Both choices depend on timetable fit, luggage, late-arrival comfort, weather, and the first-night location. Keep the first evening narrow until the arrival route is confirmed.
If you only do one thing
Use the Como bus corridor when western-shore arrival is straightforward. Use Varenna rail plus ferry only when train access clearly offsets the extra crossing and the final ferry layer is secure.