I own both and both are fantastic. For me personally, it is a complete coin toss. Batman 66 is so deep that I find myself playing it over and over just to try out different approaches, minor villains, etc. Attack From Mars is always fun, but less deep. That being said, I play it over and over as well.
Of note, whenever I have others over, Batman 66 barely gets played versus AFM. It is simply not as approachable or fun for the non-pinhead.
Ultimately, you can't go wrong with whatever you decide.