Best place to get rental car

This past May we were in Varenna, then took the train to Verona for a few nights, then rented a car for several nights in the Dolomites, then returned it to Venice. That worked for us since we didn't have time to explore the area between Varenna and the Dolomites. I believe the one place to rent a car to drive to the Dolomites from Lake Como is Lecco.
After renting the car, we stopped in Bolzano to see the Ice Man on our way to Ortisei. Leaving Ortisei on the way to Venice, we drove the Val Gardena pass which was spectacular (as a passenger, the driver has their work cut out for them, but I'm told it is fun.)
The Hertz rental is pretty close to the train station in Verona, but we took a taxi from our hotel, so I can't attest to the distance.

Taking a train from Lake Como, you'll be changing trains in Milan Centrale. I'd suggest taking one of the fast trains all the way to Venice from Milan--since it's only about 2:35 hrs..
Last time we came into Venice driving south through the Dolomites, we came in from the north--staying in Udine, Italy--50 miles or so NE of Venice. That's a good way to get into the mountains from Venice too.
Northern Italy is absolutely beautiful, and you're right to see it by rental car.

We'll be staying in the Dolomiti so the train straight to Venice won't work. Thanks though David. Good info about renting a car in Lecco. That would be easier.

Are you going to Varenna upon arrival?
If so why don't you rent a car at the airport and drive to lake Como directly from the airport?
If you flew to Reno to visit Lake Tahoe would you rent a car from the airport and drive to the lake or take Amtrak to Truckee first?

In the circumstance you mentioned, my suggestion would be to travel to Varenna by train and then rent the car in Verona. A few thoughts.....

• It's not a good idea to get behind the wheel right after a long international flight, and while suffering jet lag. That's a practice that's been compared to driving while impaired.
• If you're just going to explore the mid-lake area, you'll be using Ferries most of the time, so the car will be useless, gathering dust and incurring rental charges during your stay in Varenna. For example, if you plan to visit Bellagio or Menaggio, it makes more sense to take the Ferry rather than driving around.
• Parking can be "challenging" in Varenna, depending on where you're staying. There will of course be a cost for that.
• Travel from Milan to Verona will be faster by high speed train than by car (as short as 1H:23M).

Keep in mind that each driver listed on the rental form must have the compulsory International Driver's Permit, which is used in conjunction with your home D.L. These are valid for one year, and easily obtained at any CAA/AAA office (two Passport-sized photos required, which may be provided by the issuing office). You may also want to have a look at some of the other posts here concerning the dreaded Zona Traffico Limitato areas that are becoming increasingly prevalent in many Italian towns & cities especially Florence, which is almost saturated with automated ZTL cameras. EACH PASS through one of the automated Cameras will result in a €100+ ticket, which you won't know about until several months after you return home!

I don't prefer the Milan-Verona train option since you miss a chance to drive through more mountain scenery in between your two bases. I vote for renting either at the airport (especially if you need an automatic transmission car) or at Lecco (if a few days later makes a significant price difference).

I'm for renting a car at the airport, because that way you can get to the Dolomites via the Stelvio Pass and Merano. Renting in Lecco would require some, albeit little, backtracking, but if the price difference is not substantial I'd go for the airport rental. If you can't drive manual transmission I wouldn't chance picking up a rental in Lecco.

Thanks everyone for your input. They've decided to try renting in Bolzano.