64 controls like shit by today's standards, and level design is very hit or miss, IMO. 3D Land is (relatively) timeless because it has an actual vision apart from pure novelty (64's novelty was from being the first 3D platformer, and it succeeded very well in this regard... when it was released). 3DL takes an approach to 3D platforming that hasn't really been done before and basically perfects it in terms of gameplay. Its main problems are that it's too easy for a large chunk, and feels barebones in some respects. But it controls like a dream and the level designs, while short, are consistently excellent and engrossing. It never feels like a slog, which describes how I feel about Mario 64 for most of it.
If you asked me to compare how I felt about 64 in 1996 versus how I felt about 3DL in 2011, I would rank 64 >>>>>>>> 3DL. But if you asked me to play one or the other in 2013, it's not really even a decision I'd have to think about. 3D Land, any day of the week.