What's the best train route from Vernazza (Cinque Terre) to (Lake Como)?
 

We would like to travel from Vernazza mid morning to Varenna. I understand we will need to change trains in Milan. Do we go through La Spezia or take the little train from CT to Genoa first?

Just go to trenitalia.com and pick the route that takes the fewest hours to get into Varenna.

example: 10:27 will get you into Varenna at 3:23--just under 5 hours.