Yeah, I'm going to echo the others on this one. I don't really think that a 3D version of ZC is going to be as accessible as you think it is. Rather than argue the whole thing, let me try something else.
SketchUp is probably the 3D tool with the lowest learning curve to get to the point where you can make a N64-styled 3D environment. Let's say that hypothetically, we had a tool to painlessly import a finished level model from SketchUp. I would like you to go download SketchUp and whip up a small area. Design something along the lines of Kokiri Forest or Kakariko Village. Room to wander around, plenty of little niches and places to hide secrets without being too unnatural-looking. Don't bother modelling the inside of the buildings or whatever, just a single location.
Once you have that done, keep in mind how long it took to do and how much work it was. Now, let's play-test it. There are a handful of fairly easy to use importers for Super Mario 64. It's not the same game, but it's an engine that's on par with what you're wanting to do graphically. It should be as close as you can get to plug-and-play. I'm pretty sure that it's simply having the importer patch the rom automatically to allow level imports, then replacing locations. Load up your model, and run around the area you made to make sure that it plays how you want. Know that you're going to have to make adjustments for playablility, and that editing a 3D model to not look like an obvious patch-job is going to be more difficult than just swapping a few tiles.
Got it running perfectly? Great! Now, keep in mind how many of these areas you're going to need for even a short quest. For a very short quest that still feels like a complete project, I'd estimate something like the first child portion of Ocarina of Time, with a final level tacked on, so you would need an overworld, a few side areas, three main dungeons, and a final dungeon.
Don't think that I'm trying to discourage you at this point. Making a 2D ZC quest is a long process as well. However, if you're still keeping up with me here, we're almost done! Now, there are a huge number of 3D engines that can run your desired quest. I mean, we have Ocarina of Time hacking, and there are a number of easy-to-use 3D engines like BlitzSonic and stuff, so I'm sure that there's a fairly simple Zelda equivalent. Hell, show that you have a substantial idea and a good amount of the modelling work done, and I'm sure that you'd easily be able to find somebody willing to slap together a rudimentary engine for you to work with. (There are how many different variations of BlitzSonic out there?) You're obviously planning something N64-styled, so you don't need to worry much about lighting or anything beyond basic textures.
Like I said, there ARE 3D engines out there for you to use. The only thing is, they aren't as obvious as the 2D engines because the level design alone is such a big step up from 2D design. It's a lot of hard work to plan out a fully-3D environment that's fun to play through.
Even so, I'll make you a deal. No sarcasm, I'm being 100% honest here. I've been considering teaching myself how to build stuff with Unreal Engine 4. I found a website with a bunch of "idiot-proof" tutorials on the process, and I'm honestly interested in learning. Get a few models together, like a dungeon and the surrounding area, and I can sit down and see if it would work as a first project to help learn the ropes in the program. Best offer you're probably going to get on this site, honestly.