Mestre or Venice for our family ?

I would stay at the airport and rent the car there. Perhaps something like the Marriott Courtyard. Shuttle back to the airport, pick up the car, go and get the family at the hotel, and off you go (Day 3). Day 1 arrive and check in. If you want take the bus to Venice for a bit you could if you have time.

Day 2 bus to Piazzale Roma in the morning, catch the vap to Burano, or even take in St. Marks, then vap to Burano, then return. I don't know if you can go directly for the airport to Burano but I wouldn't be surprised, check it out.

Mestre isn't much, but then you aren't there very long. But, I would stay at the airport.

Since you are arriving in the morning, consider that you may not be able to check into a hotel until the afternoon, wherever you stay. So you could just use that time to move on to your next real destination.

Why would the first day be lost? You arrive early, wander around Venice, have a nice lunch, wander some more... And if you're very tired have an early night, but throw away a Whole day is a waste!

Most people say that staying active on their arrival day helps them get over jetlag more quickly, so don't write it off as a lost day. Since I'm not aware of any tourist oriented sights in Mestre, staying active will be easier if you stay in Venice. Personally I'd look for a hotel near Piazzalle Roma since that's a good location to pick up your rental car. There have been recent favorable postings about Hotel Santa Chiara, which is closeby (use search box at top of page). That location also allows you to easily walk or take a vaporetto to other parts of Venice. While you might consider a vaporetto pass for your entire stay, it will definitely pay for itself the day you go to Burano. If you buy the pass at the airport, you can add the bus to Piazzalle Roma cheaply.

If you decide to stay in Mestre, there are frequent regional trains to/from Venice for 1.30 euro each way. Avoid the Freccia trains which cost 15 euro for the 10 minute trip. If you stay near Piazzale Roma, be VERY careful about observing the speed limit as you drive across the bridge from Venice to the mainland. A few speeders have reported getting 3 tickets on the bridge, one from each of the automated cameras.

thanks for the answer and the advices !

Hotel Santa Chiara is 590 euro for 2 nights. No thanks.

Look at Hotel Santa Lucia also called
albergo santa lucia which is close to the train station but down a quiet lane so no crowds by the hotel It has outdoor tables and is comfortable and clean. .
It is also near vaporetto stops. We enjoyed are stay there.

If you can't find an affordable hotel near Piazzale Roma in Venice, then I'd say get one in Mestre, as close to the station as you can, and use that very low cost local train to get in and out of the city. You could do that on your first day to give the kids a taste of Venice. Head over to Cannareggio or down to Dorsoduro on foot to avoid the vaporetto fares.

For Burano you'll need a vaporetto or the Alilaguna ferry. Unfortunately there's no direct service between the airport and Burano, so you'll need to go there from Venice, or on two separate Alilaguna lines if you're staying near the airport.

If you need to take the train back into Venice on the third day to get the car, then so be it. Shouldn't be too difficult. But your Mestre hotel might be able to help you find a nearby rental office to save you that short train ride.

You might want to consider staying in Padova (Padua) if you absolutely can’t find something on the islands of Venice. I wouldn’t stay in Mestre. You can take either a train or airport bus to Padova. That town has several nice places to walk and sites to see your first day. Then head back to Venice by train your next day to Venezia St. Lucia.

You could pick up your car the last day in Padova.

First lodging that came up on Booking. com for your dates in Padova City Center: Appartamento al Duomo for $178 total for two nights. Rating is 9.4, number of reviews is 49.

Have you looked at monasterystays.com? I went to Venice this October for a week. I had a private room with a private bathroom (both very big and newly renovated). A/C and heat, wifi, and simple breakfast (cereal, yogurt, coffee, pastries, bread rolls, nutella and honey, some fruit) included. The fridge was stocked with bottled water (still and sparkling) free for guests. I paid 70 Euro per night. The monastery was in the Cannaregio neighborhood, quiet and away from the crowds. About 20 minute walk to the Rialto bridge.

Casa Vacanza Madonna dell'Orto Patronato Pio IX
https://www.monasterystays.com/

As you're planning to rent a car, be sure each driver that will be listed on the rental form has the compulsory International Driver's Permit, which is used in conjunction with your home license. Also, you'll need to be extremely vigilant to avoid the ZTL (limited traffic) zones which exist in many Italian towns. *EACH pass through one will result in hefty fines. Do NOT drive into Florence!

The ~12 minute trip between Venezia S. Lucia and Venezia Mestre costs €1.30 per person. Don't forget to validate locally purchased tickets prior to boarding the train, or again, hefty fines.

I’d still stay in Venice, if at all possible. You get in at 10:30AM, meaning you could be in Venice by 12-1 easily. Drop off stuff at the hotel, see a few things (you will be tired, but can still enjoy a walk, see canals, etc. Being outside helps with jet lag!). The next day go to Burano, then on your departure day get your car and leave. Easy.

If you arrived at 10:30PM then Mestre makes more sense. Here you have 3/4 of a day that you need to enjoy - staying awake and doing something fun.

If you can’t find anything affordable in Venice, is Burano a must? You could go straight to Verona or Padua from the airport, spend time there, then get your car there when it’s time to move on.

3) what would I do? After seeing Venice from the air, I'd like to see my kids' faces as we vaporetto from the airport and approach Venice :) What a fun and invigorating first impression! Hotel or Airbnb IN Venice, should be able to arrive by noon via Alilaguna. Stay active on arrival day by visiting (you said no San Marco) piazza S. Maria Formosa, SS Giovanni e Paolo basilica, Cannaregio. You mention Burano on day 2, I'd start at Torcello, then vaporetto stop at Mazzorbo to walk across isola Mazzorbo to Burano. Enjoy Venice by evening; my kids loved Venice after dark. For day 3, take the vaporetto along the grand canal up to P. le. Roma to pick up rental car.
We took our "kids" (in their 20's) last year and they all loved Venice. For us, an apartment was the way to go for our family of 5. In fact next time, I will spend just a bit more to taxi boat from the airport instead of vaporetto.