Why would you prune the tops off? I usually pick the really low blooms off as tomatoes at ground level may rot on the ground or get eaten by *something*, but for pruning the rest it's about how tall you want the plant, if it's staked how high it can be supported and whether you're trying for something that looks like a vine or a bush, which can depend on how much space is between each plant. Tomatoes do have a harder time getting large fruit high up on the plant but if you don't have enough growth down low, that's where the rest of the fruit will have to be later.
Personally I leave everything including the suckers for the first 18" or so at the bottom then pick off any suckers higher up, then once the plant is over roughly 10" taller than the stake it's tied to, I cut off anything that looks like it's going to flop over sideways if it tried to grow fruit.