Northern Italy Honeymoon (Tuscany, Cinque Terre, Venice, Lake Como?) - end of May/early June

First of all, where are you flying into Europe from?
With the interests you show, your best bet might be to book a room on an agriturismo (working farm) south of Florence and do day trips out of there by rental car. Siena, San Gimignano and Volterra are close by, as are some of the great wine cities like Montalcino.
With the time allotted, you might be just limited to a couple of locations--Florence area & Venice. Most people bypass Pisa as there are more important cities in the area to visit.

With tne time hou have, you need to eliminate some places. You sound like Tuscany would be a good fit and villas are available for rent. Rent a car and explore! Lots of wineries. We prefer to stay in. Hianti refion, , others prefer sfaying near Montalcino and Pienza. All are wonderful. Do a full day trip to Florence. Give Tuscany a full week and then add Lake Como or Venice.

It is often recommended to fly into Venice (as opposed to out of) because the flight times are often horribly early--and what better place to start off a honeymoon? I would stay no less than three nights.
Look at train schedules on the Trenitalia website. It's a bit cumbersome to get from Venice to the Cinque Terre, so you might consider visiting Florence next, and/or the smaller Tuscan town of your choice, and finish up in Cinque Terre--that is if there is time. Check flights out OF Genoa and Milan as well. I have to tell you Cinque Terre is very crowded, so if you are going to drop a location, that is what I would choose. Lake Como could be your consolation prize.
If you are not comfortable driving, Siena would probably make a good choice, or Lucca.
Keep reading and fine-tuning exactly what you want out of the trip--congrats!

Milan is a major air hub so you are likely to find more options (with fewer transfers), and possibly cheaper flights from there, rather than the small airports like Florence.

I think the advice given by Valaphiladelphia is spot on. My idea of a honeymoon is a time to relax, so I would not want to be rushing from one destination to the next. Given your dates it looks like you have 12 days. Assuming you fly into Venice and depart from Milan, I would suggest:

Days 1, 2, 3: Venice

Days 3, 4, 5, 6, 7: Agriturismo or villa in Tuscany / Florence area

Days 8, 9, 10: Cinque Terre

Days 11, 12 (or just your last night before departure): Milan

Best wishes for a lovely wedding and many years of happiness together!

I'd select Piemonte over Tuscany. I like their wines much better and Tuscany IMO is overrated. You could stay in Asti or any other cute town there.
I might fly into Milan or Florence spend a couple nights in Florence
Head Piemonte and spend 3 nights
Lake Como (most romantic place in the world IMO) stay in Bellagio spend 2-3 nights
Venice - remained of your time there and fly home from there.

We have spent time in all those locations and visited the CT, Sienna (which I do love)

We found flights cheaper in Florence September 2017 than Milan or Venice

Thank you everyone for your suggestions and all the help! It definately helps us get a good start to planning :)

So now we are thinking to go from NJ, USA to Venice --> Tuscany/Florence -> Lake Como --> then go to Milan the full day before our flight and depart from Milan.

[Thank you @epltd for the breakdown :) ]

Days 1, 2, 3: Venice (land early afternoon Day 1 and leave day 3 evening)

Days 3, 4, 5, 6, 7: Tuscany / Florence area (arrive late night Day 3 and leave early morning day 8)

Days 8, 9, 10: Lake Como (get to Lake Como early afternoon Day 8 and leave evening Day 10)

Days 10, 11: Milan (get to Milan late Day 10 and leave for flight early Day 12).

We read up on Cinque Terre and how it can get packed sometimes, so decided we would rather do Lake Como and do more of a relaxing feel. Anyone think a day trip from Florence to CT is worth it?

Thanks!!

Unless you have something particular in mind for Milan, one night will be enough. You could add that day to Tuscany. I'd work on fleshing that part out now---how much time in Florence vs a smaller town, car or not, etc.
Once you get the Tuscany part sorted, we can make suggestions on the coastal day trip, but I don't think a day trip to CT is worth the travel time, plus then you have to contend all of the other day trippers. You'll be back!

Congratulations! What a great honeymoon you are planning!

After you arrive from your overnight flight, you have 11 nights, (if you organize your trip by nights instead of days, you get better idea of free days vs travel days) . you say that you want food and wine and relaxation, so the first thing that occurs to me is that your newest plan has 3 or 4 travel days built in (is Tuscany/Florence 2 stops or 1?). So, how about:
Nights 1,2,3 Venice (so romantic a great choice)
Nights 4,5,6, 7 Tuscany (lots of lodging, cooking classes, wine options here)
Nights 8.9, 10, Florence (if you're not into art and museums you could make it 2 nights here and add one more above to Tuscany)
Night 11 Florence or Pisa (flights to the US are often cheaper from Pisa, but you'd either have to spend the night there or build the 1.5 hour train ride into your flight plan)

This gives you only 2 (or 3) "travel days" which puts your relaxation level high. Rent a car at the train station in Venice, travel to Tuscany for your time there, and drop the car in Florence.

Just some food for thought!

I'm guessing that Milan is your best option for a flight home. I'd take a night away from MIlan and add it to Venice. Give yourselves time to relax, get over jetlag and enjoy the city, spend at least 3 nights there. I don't know what there is to do in/around Lake Como, so I don't know if 3 nights there is enough or too many.

Without a car in Tuscany, you are probably better staying in Siena or Florence. Siena's a bit quieter, but not as convenient for transportation. You could find a small apartment in Florence, maybe in the Otrarno area, less touristy, more locals/residential, but still close to everything.

I just want to add that we did CT as a day trip from Florence. It was a long day but we hiked all of the towns and it was a fabulous tour and I was glad we did it that way as opposed to staying there. Highly recommend.

In terms of flight logistics at that time of year, from Newark airport you will have nonstop flights to Rome, Milan and Venice, and from Philadelphia airport you have nonstop flights to Rome and Venice. If you want to fly anywhere else in Italy, you'll have to change.

Many flights from Venice back to the US that involve connections will leave Venice airport very early in the morning, and getting to the airport early is expensive, a big hassle, or both. However, the nonstops back to Newark or Philadelphia leave later. So, the usual caution about avoiding flying out of Venice does not apply if you get one of these flights.

You won't want to drive on your arrival day, so an easy thing to do is arrive in Venice and spend 1-2 nights there. Then, pick up a car in Venice (from reports here, don't go even a single mile over the speed limit on the causeway leaving Venice) and drive around. Spend your last night near your departure airport (doesn't have to be in the city itself, but you don't want to miss that flight, so make sure you have some "cushion" to get to the airport if there's a problem that morning). Rome is farther from your area of touring the other airports mentioned above (Florence, Pisa, Bologna), but it has the nonstop flights, so you may prefer it. In addition, train connections to Rome for further north, if you don't want to drive. For the Rome airport, you can stay at an airport hotel, or in central Rome; from central Rome, there are various easy options to get to the airport the morning of your flight.

We read up on Cinque Terre and how it can get packed sometimes, so decided we would rather do Lake Como and do more of a relaxing feel. Anyone think a day trip from Florence to CT is worth it?

You can, it'll be a long day but, you're young and excited so go for it. One-way transit time would be 2.5-3 hours depending on route, will require a train change in LaSpezia; you will be on the train likely 6-hours total for the day. Catch the earliest train out of Florence to get ahead of the crowds, and give yourself enough time to hike/walk between a couple of the villages. Pack a water bottle and some bites as both hiking and on the train ride you'll likely want to nibble, eat lunch in one of the villages. Train ride back, it'll be you and 300 others who are doing the same thing, everyone will be wiped-out and sleeping on the ride back. At the end you can say you've been there, if you liked it, you know what you saw and can always plan for the return trip.

I just want to add that we did CT as a day trip from Florence. It was
a long day but we hiked all of the towns and it was a fabulous tour
and I was glad we did it that way as opposed to staying there. Highly
recommend.

Lori, unless you did it quite a long time ago it's not really possible to hike to "all" of the towns in one day if coming from Florence. Two legs of the 7.5-mile costal Sentiero Azzurro route have been closed for quite some time and will remain so in 2019.

We did stay in the CT and never regretted that choice as the early mornings and evenings were the best times to be there.