Both are truly fun games that I played endlessly as a child. I have favorable memories of both, but I think 007 is the better game. MK is undoubtedly fun, but 007 is superior in other aspects - longevity/replayability, story, impact etc.
Really a tough match-up here. Both are on an equal field in the fun factor, but when you talk about technical merits, 007 shines above MK.