There are really two ways to approach baseball salaries; normatively and positively.
Positively, the correct salaries are whatever the market will bear. Demand drives pricing, and MLB players are in demand in a way that MLS players are not. Positively, baseball players are payed appropriately.
If we want to make normative statements (i.e. what baseball players "should" be making), then sure, baseball players are overpaid. Why are guys who hit balls with sticks for a living making orders of magnitude more than firemen or teachers or even doctors? As soon as we open this door, however, the same would be true for every other sport and lots of other things, and we're basically reshaping the entire economy in fantastical ways that have no bearing on current reality.