Intake is my vote, here's why:
You want positive air pressure in your case. Even though the HAF has all kinds of grills and such to let air "seep" in all over, its still better to have an abundance of cool air being pumped into your system. Furthermore, you have 2 exhaust fans that are expelling loads of air. 2 vs 1, you do the math. If you're sensitive to system noise, you may want to look into purchasing a quieter fan
than what came stock with your case. I would try it with the stock fans first though.
Also, your intake should be in the front of the case, and the exhausts at the top and rear. Not sure if you just explained that wrong or what.
Main: i5-3570K, ASRock Z77 Pro4-M, Asus GTX660 TOP, 500GB Crucial BX100, 2 TB Samsung EcoGreen F4, 16GB 1600MHz G.Skill @1.25V, Silverstone PS07B
HTPC: A8-5600K, MSI FM2-A75IA-E53, 4TB Seagate SSHD, 8GB 1866MHz G.Skill, Hand-Built Wood Case