Unless you have a lot of time in Rome, or are there for a second time, you should select either Ostia Antica or Pompeii to see and skip the other one. Both towns have a central square of public buildings, a great theatre, a bath house, and a decent on-site cafeteria about half-way through your visit. Pompeii has many houses in neighborhoods to see, Ostia Antica has fewer and is mainly public buildings. Pompeii was a wealthy city, Ostia Antica was a port city populated by the working-class. Pompeii is better preserved.

It will cost you €66 and about 5 hours total for the train ride to Pompeii and back. It will involve switching trains in Naples. It will cost you €3 and about 90 minutes total for the metro ride to Ostia Antica and back, all on the metro, with one switch of subway trains at the Piramide station. So if you're on a budget, or your time is very limited, or you doubt your ability to use the train system in Italy, or you've already seen Pompeii, select Ostia Antica over Pompeii.

Pompeii is a city you mainly see whereas Ostia Antica is a town you often explore. By this I mean that Pompeii is thoroughly barricaded and roped-off so you can't touch or step on things you might harm. Buildings you aren't permitted inside have fences or barricades. Permitted routes and open buildings are shown on the guide map. On the other hand, Ostia Antica is much more of a do-it-yourself site. Routes through buildings are rather haphazard, sometimes you'll walk completely around a building through tall grasses to find an entrance, and on the way you'll "discover" something interesting that's not on the map, but which you might be able to walk into to explore further. As I remember, a sign near the entrance to Ostia Antica asked me to avoid walking on mosaic floors so I don't harm them. In Pompeii the mosaics were always roped-off to prevent damage, and were often replicas since the originals had been taken to various museums.

Having said all of this, if you have the time available and don't mind the extra expense, I found Pompeii to be the superior of the two sites. But Ostia Antica is really not far behind, and if you only have time or money to see Ostia Antica, you shouldn't feel like you're missing anything significant. Both sites will give you a good idea of life in an ancient Roman city.