Woodburner's right in that the Heller (and Revell) kits are based on old reconstructions (even earlier than the 1920s I think - at least in the case of the Santa Maria). So little is known about those ships, though, that even the most current efforts to reconstruct them can only be labeled the latest in a series of speculations. (It's certainly true that most of the more recent reconstructions have given the Santa Maria a triangular-shaped, overhanging forecastle deck, but no historian in his right mind would say he was sure the real ship was built that way.)
I think the book Woodburner mentioned is the one by Xavier Pastor in the Anatomy of the Ship series, published by the Conway Maritime Press. I don't have a copy of Mr. Pastor's book, but it's described in Cogs, Caravels and Galleons, the relevant volume in the Conway's History of the Ship series, as containing "the evidence available for the tentative reconstructions of Columbus' three ships." That sounds to me like a fair description. (Reading between the lines, the fact that there's nothing negative in that bibliography entry can be considered a pretty strong endorsement. The editors of those History of the Ship volumes tended to be pretty ruthless.)
But there just aren't enough contemporary representations of such ships to enable more than an educated but highly speculative guess. That's one big reason why, personally, I've never been particularly attracted to them as modeling subjects. There have been lots of learned arguments about them over the past century or so, but I frankly question whether the arguments are worth the trouble. The one thing of which I'm fairly certain is that if we were transported back to Palos in 1492, we'd be surprised at what those three little ships looked like.
To my eye (based on memory of models that I haven't actually seen "in the flesh" for a long time), the fact that the Heller Nina and Pinta kits use the same hull makes the idea of displaying them alongside each other impractical. (We don't know what either of the real ships looked like, but it's a pretty safe bet that they weren't identical from the main rail down.) That's just my personal taste, though. If I were picking one of the three kits, it would be the Nina.
I have a little soft spot for the Revell Santa Maria: it was the first sailing ship model I built. Dr. Graham's history of Revell gives its release date as 1957, making it and the Flying Cloud, which was released the same year, Revell's third and fourth sailing ship kits. (The first two were the Constitution and the Bounty.) It represented the state of the art at the time, and some of its features can stand comparison with much more recent kits. The decals for the shields that hung on the bow and stern, whether authentic or not, were exquisite, and the crew figures were magnificent tributes to the sculptor and Revell's amazing pantograph machine. (Two of them also shipped on board the Bounty. I do think there's pretty general agreement that they make the Santa Maria look like a considerable bigger ship than she actually was; they're certainly on a much smaller scale than the 1/60 Heller claims for its kit, which is about the same size.)
I hate to think what that first one I built must have looked like. I was seven years old at the time. I think my dad helped me with the decals, but I did the rest myself - probably over the seemingly interminable span of two or three days. My parents, and even my older brother, thought it was beautiful. At least that's what they said. Ah, memories. If I could just remember the stuff I was supposed to do today as well as I can remember building that model - fifty years ago....
One feature of the old Revell kit I never understood: the way the gummed paper flags were designed. Some highly talented, meticulous individual rendered them as pictures of wind-blown flags in perspective, complete with elaborate "ripples." Given the complex designs on them, that must have been quite a challenge - and the artist had to do it twice, so the flags could be folded over and stuck to themselves, with the two halves lining up precisely. The flag sheets in later Revell kits (and some from other companies) were done the same way. My question is: why? What was the rationale behind mounting a two-dimensional picture of a flapping flag on a three-dimensional ship model? Drawing the things "flattened out" would have been a lot easier, and anybody capable of building the model surely could put genuine, three-dimensional ripples in a flag in a few seconds. I guess most 1957 modelers didn't mind, though.
Close examination of those old Revell sailing ship kits suggests, over and over again, that the artisans responsible for them were trying to push the capabilities of the new medium of the plastic ship model to their limits - whether the typical purchaser was aware that they were doing it or not. (How many 1950s modelers noticed that the seams between the deck and hull planks on the Constitution and Bounty were raised lines, whereas those on the Santa Maria and Flying Cloud were countersunk?)
Revell Europe currently has a "new" Santa Maria in its web catalog. Given the way plastic sailing ship molds travel around, and given Revell Europe's demonstrated penchant for reissuing old sailing ship kits without taking much interest in what they actually are, I wouldn't want to bet money on whether this "new" kit is the old Revell version or the old Heller one. (As I remember, the Heller Nina and Pinta turned up in Revell boxes for the 1992 anniversary.) If it's the former, my sense of nostalgia is strong enough to make me feel inclined to welcome it back.
Later edit: I just took another look at the Revell Europe online catalog. It contains some photos of the "new" Santa Maria kit. If the kit matches the photos, it's unquestionably the old 1957 Revell one - complete with decals, perspective pictures of flags, and crew figures.