NFL, MLB, NBA, that order.
The NBA thrives on individual stars, and being able to stand out. That's where the main cash flow comes from, and where the top guys usually stand out. I think NBA players are over-valued, and while obviously a relatively difficult schedule for us, its not the hardest out of the 3.
The MLB is second. They play 162 times in the season, through the heat of the summer. Its also the hardest sport to keep your rhythm, or to fix a problem. Anyone who has played baseball for extended periods of times know how hard it is to correct just a minor flaw in your swing or throwing motion. You play with usually only 1 break per week, that typically being used as a travel day. The NBA gets a lot of rest in relation, allowing time to fix a hitch in your stroke and rest nagging injuries.
The NFL definitely deserves the money. They bring in the most, the are the most watched, and are the most popular. The players put their careers on the line on every play, and are at an exceedingly greater risk for head and neck injuries. It involves the most strategy, and requires the highest intelligence level from the players. Every sport has its own skill level, but overall, football probably takes the cake for best all-around athletes, and sees the highest turnover rate in players not panning out. If you can make it to your prime, and play at an elite level given this, you should be paid the best.