Which train better to take to Venice from Cinque Terre

All 5 towns of CT are on the same rail line. It does not matter which town you stay insofar as getting to Venice is concerned. Any difference in total travel will be minimal/insignificant.

Here is one source to use to look at train travel--- https://www.bahn.com/i/view/index.shtml

You can either go through Milan or Florence. Check the schedules on Trenitalia's website and see which works better for you, based on total travel time, connections, and cost. Schedules might change between now and next May, but you can check schedules a month or two out to guess what they might be next year - and decide closer to departure.

Staying in a smaller CT town besides Monterosso only means you must change trains to a local train an additional time. Personally, I wouldn't let that deter you from staying elsewhere besides Monterosso.

You can go on Trenitalia.com and put La Spezia as "from" and Venezia Santa Lucia as "to". It'll tell you the routes that you'll go through to get to Venice.

I would think most trains would go through Pisa and Florence,

To Monterosso from Venice, going through Milan will be only a single train change there, even though it is a bit longer journey time. Plus, since you are using a Freccia and an IC train, you'll have seat reservations and the possibility of getting SuperEconomy tickets all the way. Going through Florence, you change at Florence, Pisa, and probably La Spezia as well. From Florence onward, you will likely be on Regionale trains with no possibility of reservations, and no discounts (even though they are pretty cheap to begin with).