for me, i take Alomar for a few reasons but i think the case can be made for both sides:
1. he was a better hitter during the bulk of their careers both for average and as a slugger and safe to say the more "feared" hitter
2. while Larkin was a good defensive SS he was not great, Alomar is arguably the best defensive 2B to ever play the game - yes SS gets many more chances and impacts the game more defensively but Alomar was the Smith/Vizquel of the 2B position. he was able to turn so many hits into outs that i think it offsets the SS advantage at least to a degree