Best transport from Santa Margherita Ligure to Ballagio on Lake Como?

Train to Milano Centrale. Another train to Varenna. Then ferry to Bellagio.

Have you looked at Rome2rio.com? There are other options. But I think the one above is best.

jan,

That's actually quite a straightforward trip. The route suggested by Frank II is about the quickest and most direct. The trip from Santa Margherita Ligure to Varenna is about 4 - 5 hours with one change, and the Ferry from Varenne to Bellagio will be about 20 minutes (not including time walking down the hill from the Varenna train station to the ferry dock).

If it were me I'd drive.... it's not that hard

I did this and took the train from Santa Margherita Ligure to Milan. Then I took a private car service from Milan. It is definitely the more expensive option but I was looking for easy at the time.

The option described by Ken is the most logical.
Train schedules are below. Enter from Santa Margherita Ligure to Varenna-Esino.
www.trenitalia.com
Don’t leave too late as ferries stop running in the early evening.
Renting a car is another option, but I will warn you that is a long drive (mostly on freeways) and the traffic on the freeways near Milan is often congested, so don’t be surprised if it takes you well over 4 hours.

We drove, easy.