Very early planning stages and need some guidance

If you stick with returning on April 11, you have only 9 nights in Italy, which means eight full days. That is not enough to do all you list. So definitely extend to April 12. And look into flying open jaw, into Milan and out of Rome. You may find it is almost as low as the Milan round trip. I did a price comparison for someone yesterday, and flying back from Rome was only $70 more than the return from Milan. That was on SAS from Chicago, so you may find different results from your airport.

You have 9 nights on the ground, from 4/2 to 4/10 (or preferably 10 if you return on 4/12).

Considering that you are not interested in seeing Milan, the most efficient way to visit your intended destinations is to fly with an open jaw ticket with arrival in Venice then fly back home from Rome.

For example you could do:
4/2: Arrive Venice (VCE)
Visit Venice area: 3 nights (4/2-4/4)
4/5: Train Venice to Florence (2 hrs)
Visit Florence/Tuscany: 4 nights (4/5-4/8)
4/9: Train Florence to Rome (1.5 hrs)
Visit Rome: 3 nights (4/9-4/11)
4/12: Fly back from Rome (FCO) to NYC (JFK, EWR).
(Reallocate nights depending on your personal interest)

Given the short amount of time, I don't recommend flying to/from Milan. Traveling by train isn't free. Also it will waste a full day to your already short vacation because you have to take the train back to Milan the day before the return flight and spend the last night in the Milan area (the return trip is in the AM, therefore you must be near for the night).

If flying to Venice and return from Rome is too expensive, then try fly to Milan and return home from Rome. The trip from Milan (MXP) to Venice isn't too long (about 4 extra hours). However if the savings aren't substantial there is no point. Time is money and the train isn't free either.

Thank you for your replies. I priced flying in and out of different airports and it is double the price. We can fly into to Milan for about $700 per person. So if flying into Milan is the only option, what is the most logical part to cut out?

Easter Sunday in 2015 is 5 April. We were in Italy and Rome this spring; how I chose the epicenter of Christendom during that one week escaped me until I realized my calendar had Easter on the wrong date. The city was crowded, and I can only assume it was more than usually so owing to the holiday. I do know that hotel rates took a significant leap. It is probably a good idea to start planning. As for trains, you might consider Italo in addition to Trenitalia if they cover your routes. We were very pleased with Italo...easy website/ordering, well priced and friendly service. Good luck.

As has been pointed out if you must fly to/from Milan you will lose days traveling to/from Milan on what is already a short trip.
Add up the hours and the cost of trains and it might be worth the added expense of a flight to Venice/home from Rome.
Try to give yourself at least 3 nights in each location- that is still only 2.5 days. 3 nights is the bare minimum I would want for Florence and Venice, Rome needs more.

Otherwise- I'd cut a city- I'd have a hard time picking which one of those 3 as we loved them all!

Time is money when your time on the ground is so short.

If you are finding double the price is that because you are looking at one way fares into the inbound airport and one way tickets from the second airport home?

The way to do it is using open jaws, or Multi-City which should be nearly the same price as round-trip to the one place.

It doesn't work if you do one ways and add them together.

What does jaw mean? I was using multi city when pricing.

Yes Open Jaw is same as Multi City.
How far are you from Newark?
TAP has flight from Newark to Venice, Rome to Newark 1115 RT on your dates.

But if that $700 you posted above is RT I don't think you can beat that!

I'll go along with the others that you need to cut something out. 4/2 is essentially shot as you'll be collecting luggage, getting from Malpensa to your next destination, finding your hotel and checking in, getting settled and acclimated… it all takes time, plus you'll be jet-lagged.

Try like the dickens to work in that extra day and fly home on the 12th? That leaves you 4/3 - 4/11, or 9 full days. If you end up flying RT from Milan, I'll recommend going back to Milan and staying in the city the night before your flight (4/11) so then you'd have 8.

I dearly love Rome but in this case I think I'd choose just Florence and Venice, take a few day trips out of Florence, and do it all by public transport (train). You don't want or need a car in Venice or Florence, and day trips by train (or sometimes bus) are so easy from Florence.

If you could work an open-jaw ticket and fly home from Rome, then maybe you could add it but it would still be a lot of moving around in a short time.

If an open jaw is much more expensive than a round trip NYC<->Milan, then go for that one. But then you need to cut down something.
You can still go straight to Venice upon arrival.
so:
Venice: 2 or 3 nights
train to Florence
Florence: 3 nights
Train to Rome
Rome 3 nights
train back up to Milan
Milan: 1 night before the flight back.

That's the only way. Not sure if you have much time for Tuscany. 3 nights in florence are 2 full days. Maybe a day for Florence and a day as a day trip somewhere nearby (Siena, San Gimignano, or Chianti?)

Consider that the train from Rome to Milan is over $100 per person, plus the last night in Milan is going to cost you another $200 (if you are not interested in Milan it's a wasted night). Therefore you should choose the RT option over the open jaw only if the price difference is at least $200 per ticket.

Are we better off by car or rail?

You won't need (and can't use) a car in Venice and Florence.

So torn on what to do. The $700 RT pp to Milan is hard to pass up. Rome for us would be a must see. Perhaps we should elininate Venice or Florence. What is the best website to estimate the train fares?

Use Trenitalia to estimate train fares, but play around with dates to see how it works. If you book far enough in advance (90-120 days, I am not sure which) you can pretty much count on getting the super Economy fare on the fast direct trains. This will be either 19€ or possibly 9€ per seat. No further discount for a child but at these prices you cannot complain.

I assume these are direct flights you are looking at. Most flights from New York arrive pretty early in the morning. You could easily travel to Venice that day, but you need to be careful in booking the train tickets to allow enough time. The Super Economy tickets are non-changeable and non-refundable. For this one leg, you might be better with a ticket that allows one time change in case your plane is late. Milano Centrale to Venice is 2.75 hours by train.

You should be safe with the super economy tickets for Venice to Rome and Rome back to Milan, so each of this legs would be €57 for three of you.

As Roberto noted, you would likely need to travel to Milan and spend the night there before your flight. So check on Milan hotel prices as well. Sometimes the chains ( like Uma Hotels) have good deals on weekends.

I saw fares to Italy (Into Venice, back from Rome) earlier this week for $700 for next April and was very excited until I actually tried to purchase them--they were really $1350, which is what I had been seeing all along. So you might go as far as you can without actually booking anything to see what the actual cost is, then see if the multi city fares make sense. I went ahead and booked them, so I will be writing in with my own questions.

I like this site:
http://www.rome2rio.com

Since Rome is a must, I'd look at travel time from Milan to Rome -3 hours
Give Rome at least 3 nights- go straight there from Milan, 4 nights would be better since your first day is jet lag and train trip

Look at travel times to/from Florence and Venice.
Rome to Florence 1.5 hr or Rome to Venice 4hr
Florence to Milan about 2 hr, Venice to Milan about 3 hours

I'd want to spend the least amount of time on trains, more time touring, so I'd have to drop Venice, as much as I loved it. You should make your own list of what you want to see/do and pick the city that interests you the most.

You mentioned Tuscany- although not in Tuscany, Orvieto is an easy stop between Rome and Florence that would give you a small hilltown experience.

Arrive Milan- train to Rome
4 nights Rome
Train to Orvieto
1 night Orvieto
Train to Florence
3 nights Florence
Train to Milan
1 night Milan
Fly Home

I flew from Boston to Venice, spent nine nights in Italy, and then returned to Boston from Rome last March for just over $1,000 per person. We did 3 nights in Venice, 2 nights in Florence, and 4 nights in Rome. In my experience 9 nights is fine for 3 cities, and the two train rides in between were easy (pack lightly). You have plenty of time to watch the airfares and get a feel for the train fares. I loved Italy and hope you do too.
Cynthia