Where to go?

I'm not sure what lakes Ralph is referring to, but if it is the Lake Como area it is nowhere near Tuscany, which would include Florence and Pisa. Maybe he had other lakes I am not aware of in mind? I liked the Cinque Terre, but it depends on what time of year. It is all about being outdoors there. It would be easy to spend 4-5 nights in Tuscany and 3 nights in the CT if weather permits. If you would have a car in Tuscany (not needed in CT) you could base at an Agriturismo and day trip to hilltowns and to Florence and Siena. If you plan on traveling in cooler months I would skip CT and spend the entire time in Tuscany/Umbria. You could split the time between northern Tuscany and southern Tuscany or Umbria and do day trips from there. I could easily spend 7-8 nights in Tuscany and Umbria and not run out of things to do!!

I would not waste my time to go to CinQue Terra. Just left there, spent 2 nights and 2 nights too long. Hard to get too and gets boring real quickly. Sorrento is absolutely beautiful and you can visit Capri, Amalfi, etc., while there.

First of all, I don't need to look at a map to see where the lakes are located. I have been there. The OP has just spent 4 nights in Varenna (if you look at a map it is at Lake Como) and implies she is looking for something DIFFERENT. She even mentions the places they are trying to decide between. Maybe you missed that Ralph. Also, if you check train schedules you will see that taking the train from Varenna to Florence takes a minimum of 3:30 hours. That is each way. From Varenna to Pisa takes even longer at a minimum of 4:51 hours each way. I would guess that 99.9% of the people who are looking for advice as for where to stay would object to 7+ hours of commute time to do a day trip. Actually, you might be the only one reading this that would find that base and those day trips to be something reasonable to consider. Maybe you are the one who should consult a map Ralph.

It wasn't clear what lakes were being refered to as Italy has more than a few. Everyone is entitled to their opinion and to make suggestions. My opinion is that basing oneself 7+ hours round trip from the suggested day trip locations would not be the best use of valuable vacation time. Some people are geographically challenged and I would hate for Terri or anyone else to think that doing something like that would be a good plan based on anyone's suggestions.

We are looking for a different region other than where we were (northern Italy). Out of the 3 areas we went to, varenna, Verona and Venice, we liked varenna the best. With that said, we are looking for an area with that type of feel and do like being near water. I suppose that comes from living in a desert! I noticed there are a couple of lakes in theTuscany/Umbria area. Anyone stay near Lake Bolsena or Lake Trasimeno?

I posted some ideas on another post today. someone asked which regions to visit in Italy next. Take a look there. Regarding your 3 options, you can easily fit the Cinque Terre in a Tuscany trip. The 5 terre are in Liguria, but a very short distance from the Tuscan border. By train (or car) from Pisa is a breeze. So the choices really are 2: 1-Tuscany (incl. 5 Terre)plus Umbria (however 7 days are too few for this, imo)
2-Campania (Amalfi Coast+Pompeii+Naples). That's really up to you. However in terms of bases: For option no. 1 I'd choose 2 or 3 bases: one in Eastern Tuscany (Cortona?) or Umbria (Assisi?), one in Central Tuscany (Florence maybe, which has easy transport links to everywhere) and maybe a 3rd base on the coast. I would do Pisa+Cinque Terre together in 2 days max. Pisa has only one piazza to see (Piazza dei Miracoli) and 5 Terre is a one day getaway. I wouldn't spend more than a night in 5 terre. For Option 2. I'd stay in Positano, a real gem in the Amalfi Coast. From Positano you can visit the entire Amalfi coast by bus or car. They also have daily boat excursions to Capri and the Grotta Azzurra from the beach. That's what I usually do when I go there. From Positano you can also easily reach Pompeii in less than an hour. Naples is a big city and certainly deserves a visit. But I never spent a night there. Somehow I prefer the magic of Positano or even Sorrento and use that as a base. I usually visit Naples on my way in or out to/from Positano.

Terri,
I agree with Ralph. I love Bologna. Have been there 3 times. I also love Lake Maggiorie and Lake Garda. Northern Italy is great. I also have based out of Siena and Lucca. if you need detailed recommendations or hotels just let me know. I go every year and will try and help in any way that I can. I took a great cooking class in Lucca last year on my birthday.

I loved Sorrento and thought it was a good base for the Amalfi coast, since it's on the regional train line.