Rental car or trains for my itinerary

For that itinerary I would not have a car. You certainly don't want one in either FLorence or the CT. When we visited Stresa we stayed at a hotel on Isola Pescatori and of course had to find a place on shore to stash our car. We didn't use it during our stay. I'd do this with trains. We get cars when we are in places that require them e.g. a week or two in Tuscany or Burgundy or the Dordogne,but your itinerary just doesn't require and would not be enhanced by having a car IMHO.

A car for lake Maggiore (Stresa) is not a bad idea. That way you can cover more ground, including lake Orta, more easily. Also Stresa is closer to Malpensa airport than Milan, therefore in your shoes I would stay there also the last night and drive to the airport the morning of your flight and retypurn the car at the airport. That's what I do. The drive from Stresa to the airport is about 40 minutes, nearly all freeway and no traffic.
For car rental use a consolidator:
www.autoeurope.com
or the affiliated:
www.kemwel.com
They work primarily with Hertz, Europcar and Avis.
If you want to pick up at the Cinque Terre, the pick up location is LA SPEZIA, about 15 min by train from CT. The drop off location is Malpensa airport in your case. You could also pick up in Genoa, but La Spezia is closer. Or of course in Milan. However if you intend to rent a car, you might as well do it from the start when you leave the Cinque Terre. The drive is a straight shot from Genoa to Stresa on the A26. I did it last year (opposite way).
If you decide not to use a car, from Stresa to the airport there is the Alibus, or you can take the train down to Gallarate and from there a 5 min taxi ride. Either way it's about 40-45 min.

Thanks for the tips guys. I'll check out the possibility of renting from La Spezia and returning at MXP. I should have specified by the way, we're not staying in Milan the last night, we're staying near the airport...figured that was safer with a 9:30am flight.

As far as Stresa you found it worthwhile to have a car? I also like the idea of being able to stop on the way from CT to Stresa and visit small villages or take pictures or something.

I always have a car in Italy (I need it for various reasons) and I like the flexibility of having one. I wouldn't recommend one in Florence or the Cinque Terre, but to go to Stresa and staying there I would. You can do without of course, but that way you can visit more things (like Cannobio, Lake Orta) in less time. For the islands you won't need a car of course. Yes you can stop along the way anywhere along the coast, including Portofino.

Seems like europcar has some decent rates from La Spezia to Milan. Question is how can I get from the train station to the rental place in La Spezia? Taxi or will they pick me up in a shuttle(for free)? Do I need to call them, not sure I'm planning to use my cell phone over there as it's probably super expensive. Just wondering what my options are.

Thanks!

I doubt the rental car will pick you up at the station, but you can try.
Europcar is near the port on viale San Bartolomeo (which is actually very convenient to get on the freeway once you get the car and drive away).
La Spezia has 2 train stations and most trains stop in both: Centrale station and Migliarina station.
From the Centrale train station you can take a taxi (10 min ride) or a bus (L line or S line) which takes about 20 min.
From the Migliarina to the port is a bit closer, but I think the taxi is the only option as the bus will require a couple of changes. Also not sure if Migliarina has a taxi stand or if you have to call them. Centrale has a taxi stand in front for sure.
If you have luggage I'd opt for the taxi.

I would only add that taking taxis in Florence makes no sense except to/from the airport. You can, and should, walk everywhere. The sights are within a very compact area.

All - I attempted to make a reservation in La Spezia for parking, but they need a license plate number. Obviously with a rental car I won't know that until I pick up the car. Any way around this? Are there other places to make a parking reservation where I don't need the license plate number? Or will I be ok in July without a reservation?

Thanks!