Getting from Pisa to Cinque Terre

Escape,

The situation is not as complicated as you describe. It's actually very easy. I'm not sure what you're referring to as an "inter-town train"? There isn't a specific train for travel from one town to the other, and it could be any train that happens to be travelling in that direction. Not all trains will stop in each of the five towns.

Could you clarify which of the five towns you're going to be staying in. Also what time of the "evening" will you be travelling? Is there a possibility you could travel earlier in the day?

How to Look Up Train Schedules and Routes Online gives you the DB train schedule link and tips for using it. If you pull up schedules and click the arrow to see Details, then you can click on the train number to see all stops of that train. Connection point is usually only at La Spezia, not at Riomaggiore.

The actual last trains serving any of the five towns may be later than you think, as below, but confirm your arrival plan with your hotel, to know whether reception staff will be available.

Pisa Centrale Mo, 29.06.15 dep 21:36 R 11872 Regionalzug Direction: La Spezia Centrale
La Spezia Centrale Mo, 29.06.15 arr 22:49

La Spezia Centrale Mo, 29.06.15 dep 23:10 R 11330 Regionalzug Direction: Genova Brignole
Vernazza Mo, 29.06.15 arr 23:29

Duration: 1:53; runs not every day, 29. Jun until 31. Oct 2015 Mo - Sa; not 15. Aug .

OR

Pisa Centrale Mo, 29.06.15 dep 22:53 IC 522 Intercity Direction: Sestri Levante
Subject to compulsory reservation , Global price , space for wheelchairs

La Spezia Centrale Mo, 29.06.15 arr 23:54

La Spezia Centrale Tu, 30.06.15 dep 00:50 R 24482 Regionalzug Direction: Sestri Levante
Vernazza Tu, 30.06.15 arr 01:09

Duration: 2:16; runs not every day, 29. Jun until 30. Oct 2015 Mo - Fr, Su; not 14. Aug .

You can also look up schedules on Italy's National Rail website: Trenitalia. It will have schedules for all trains which run between Pisa and the CT Villages.

http://www.trenitalia.com/cms/v/index.jsp?vgnextoid=4ddd1a035296f310VgnVCM1000005817f90aRCRD

Hi. Sorry, I was not clear on this. But what I mean by inter-town is the local train that connects the 5 towns.

I understand that one can buy the unlimitted day pass for the train that connect the 5 towns. Now, is the day pass purchased in La Spezia or Riomaggiore? Do I use La Spezia as my starting point for all logistic in the region or do I use Riomaggiore, is basically my underlying question.

Escape,
As Ken noted above, there is no "inter-town" train JUST for the Cinque Terre. All of the villages are on Trenitalia routes which pass through that region - although not ALL trains stop in ALL of the towns.

So you want to use the Trenitalia website for exploring what trains are available on what day, and for around the time you're wanting to leave Pisa. You don't "have" to spend the night at La Spezia or ‎Riomaggiore: you can stay anywhere in the CT that you've made a hotel reservation as they're all served by train.

You should also just buy your ticket in Pisa but you can explore schedules/prices in advance. Just pulling up a random day (7/8/2015) and times (19:00/7:00 - 20:00/8:00 PM) and CT town (Manarola), there's a train at 19:03 from Pisa that takes 1:08 hr with one change in La Spezia. There are other trains at other times - and ALL of them will involve at least one change - but some take longer. Depending on your final destination within the CT, some may also involve more than one change so if possible, try to plan your departure time to be able to catch the quickest, most direct trains.

If you're traveling on a ticket with NO SEAT RESERVATION (standard on regional trains) remember to validate your ticket before boarding.

As far as a day pass for the trains within the CT, we purchased a 5 km pass which was good from time of first validation until midnight of that day but that's been a few years back, and I'm unable to confirm if it's still available. If so, it can be purchased at any train station in the CT. Otherwise, individual tickets are not expensive (don't forget to validate them!).

If you intend to do any hiking, you might consider a one or two-day combo pass - Cinque Terre Treno MS - which covers the fee for using the trails; trains between the villages; local buses, including the bus which travels from Corniglia's station up the steep hill to the village; public toilets; and wifi hotspots at the stations within the park. That pass must be validated the first time you use it.

A one-day pass is € 12.00; a 2-day pass is € 23.00. It covers 2nd-class train travel between La Spezia and Levanto, and can be purchased at the stations. You don't want to validate and use one of these in the evening: wait until the morning of your first full day to get the good out of them.