Latos has the lower ERA and WHIP this year, though Liriano's rocking a lower FIP and is undeniably the better pitcher when one looks at peripherals (higher K rate, higher GB rate, more swinging strikes, etc.).
Both of them are huge bargains for next season -- Liriano was a 19th round draft pick, and Latos a 23. I would have two more years (2012, 2013 options) on each.
My concern is that Liriano is a big injury risk, and that I can't rely on him to be healthy. Latos pitches in such a great home park, and is so young, that he could be one of the NL West's most dominant pitchers (along with Lincecum, Kershaw, and Ubaldo) for the next three seasons.