I am going to Italy in late May for two weeks. I am having an awful time trying to figure out whether to rent a car for the time at the Lakes/Milan/CT (one day to hike) or whether I can use public transportation. Trying to figure out train stops is a nightmare! I arrive in Milan and will base in Stresa for five days. I plan to see Lake Orta, Maggiore, Como (Bellagio and Varenna only), Bergamo, Milan (just the highlights)and CT before going to Bologna for the second half of the trip. So should I rent a car for the first five days, or can I use trains and boats?

Use the trains! I wouldn't dare drive to Cinque Terre. I also wouldn't miss CT for the world!

I wouldn't recommend CT as a day trip from Stresa no matter how you get there - it is just too far. I think Como and Bergamo would be too difficult by public transportation. Take ferry rides around Lake Maggiore. Perhaps you are being too ambitious, just enjoy being in Stresa and Lake Maggiore, take a daytrip to Milano. You could make a circular trip by rail and boat to Ancona, Switzerland via centovalli rail:
http://www.centovalli.ch/

Yes, I am planning to do the Centovalli train! I think CT may lose out this trip as I also want to see Orta and Como. It looks as if I can take the train from Stresa to Milan to Como and the ferry to Bellagio/Varenna. OK, no car -- I am convinced!

Thanks for your suggestions.

You will need a car to see all of those locations, especially Orta. I would then drive to the CT for 2 nites before going on to Bologna.