We are planning on going to Cinque Terre for 1 day in June. What is the best town to stay in to catch a train in from Pisa and out to Milan?
No matter where you stay in the CT, you will have to transfer to the main train line to get to Pisa or Milan....so it won't matter which town you pick.
As Ellen said, you could have your overnight accomodation at any of the Cinque Terre villages. To travel from the Cinque Terre to Milan in minimal time: when I was there, in 2004, there was an express train from Monterosso to Milan. I do not know at what time the train departs from Monterosso.
Monterosso is the most enjoyable town for overnight accomodation in the Cinque Terre. (and the most expensive). Some hotels in Monterosso are at locations that are not near the train station. Thus, if you are at a hotel in Monterosso Old Town,for the day when you travel to Milan I recommend get an appointment with a taxi driver for your departure from the hotel, the previous day. In Vernazza a few rooms are located within a quick and easy walk to the train station. The rooms are in an apartment building. Tonino Basso owns some of the rooms, he rents the rooms out to tourists. A very good place, big rooms. Read about it in the book Rick Steves' ITALY. Get a reservation for a room now !
We stayed at the Hotel Pasquale in Monterrosso and loved it. Beautiful views, reasonable rates, and an excellent breakfast! You can easily get to the different towns by train or boat, or you can hike some or all of the CT trail. Have fun!
Many through trains stop in Monterosso-al-Mare. Some trains will go from Pisa to Monterosso, and others will take you from Monterosso to Milan. I always stay in Monterosso at the Hotel Agave which is maybe 100 yards from the train station. There are other hotels even closer.