I went to see replicas of the Niña and Pinta today. The first question on the FAQ they hand out: "Where's the Santa Maria?". They answer: They didn't make one, and they aren't going to. It's to big to go most of the places they take the Niña & Pinta, and Christopher Columbus didn't like it much either.
Those ships are quite small for the number of people they originally had on them, and the length of the voyages they went on. The replicas have diesel engines on them and take a much smaller crew.