I'd go with Link Between Worlds on this one. I played the Gamecube version of OoT, which apparently wasn't all that different from the N64 version from what I see. Haven't played the 3DS remake, so my opinion might not count as much. I had fun with it more consistently than Ocarina and the items and weapons in LBW all had utility, which isn't something I can say for Ocarina (Looking at you, Element Arrows).
Now if it was a choice between Majora's Mask and LBW, on the other hand...