We just did the Punto Tombo and the Magdelena Island Penguin tours. Both are painful getting to and from the rookeries, but wonderful once you are there.
Punto tombo is a three hour bus ride each direction down a very boring dirt road. You can rent a car and do it on your own. The lunch provided on the ship's tour was awful.
Magdelena Island is more beautiful, however the "Ferry" ride with seven buses on board was equally painful. If you can imagine being on a bus, on a ferry. for 21/2 hours each direction, with very little visibility except the other buses on the barge next to you, you have the picture. This trip requires you take the ship's tour and the food is also inedible. You would be better served to pilfer food from the breakfast buffet line and make your own picnic, eventhough its not entirely legal.
If I were only going to do one of these, I would choose the Magdelena Island tour because the island is quite beautiful and there are greater numbers of penguins this year.