In their primes, both were great players. Larkin was the best NL SS during his time and, when healthy, you could argue he was the best SS in the ML. Alomar was the best AL 2B during his time and you could argue the best 2B in the ML.
Both were great baserunners, and their hitting rate numbers are similar. They have the same OPS+. Each made 12 All-Star games. Larkin has 9 silver sluggers and 3 gold gloves. Alomar has 10 gold gloves and 4 silver sluggers.
162 game averages
.300/.371/.443., 103 runs, 34 2B, 5 3B, 14 HR, 77 RBI, 32/40 SB
.295/.371/.444, 99 runs, 33 2B, 6 3B, 15 HR, 71 RBI, 28/34 SB
Pretty damn similar, but when push comes to shove, I have to take Alomar because he was the much more reliable player since he managed to avoid injuries (or play through them, or whatever). Larkin played 130+ games 8 times in 19 years. Alomar did it 14 times in 17 years.
It's a closer call than I'd have expected, but I have to give the nod to Alomar. On a more anecdotal level, there was a time (circa 2001), when people could legitimately make an argument that Alomar was among the very best 2B to ever play the game, at least in the modern era (to exclude Hornsby). Such discussions ceased, of course, when his career fell off the cliff in NY. As much as I like Larkin, I can't recall anyone making a similar case for him at SS.
And, finally, is no one going to question the "SS get way more chances" stuff that keeps getting thrown out here? We're talking about baseball here - they keep track of such things. For his career, Alomar's RF/9 at 2B is 4.97; Larkin's at SS is 4.62. Yes, different leagues for much of the career, but just take a look at the league-wide RF/9 for the positions of SS/2B, in either league and you'll find the same thing.