The Time Bombed Skyscraper to me is by far a better movie, why? Becasue I remember it. Having watched both only once, I remember far more about The Time Bombed Skyscraper than I do Strategy Above the Depths.
All I remember from Strategy Above the Depths is Kogoro's epic scene, but I honestly cannot recall the mystery involved. It was bland, That movie was just another "Let's put Conan in X, Y happens, then X explodes." While I can recall most of the plot from The Time Bombed Skyscraper becasue even if it wasn't a great movie, it doesn't fade away as quickly for me.
The Time Bombed Skyscraper was kind of boring as far as a mystery goes, but it was overall a better movie becasue it cared less about what would obviously be a crappy mystery, and instead focused more on Ran and Conan. Also the music was far more memorable in The Time Bombed Skyscraper.
But let's face it, the movies are really just an excuse to blow crap up, everything else is just a added on to distract from that fact, and as far as explosions go, The Time Bombed Skyscraper was much better than the lameness of a sinking ship.