If my long-term goal is to be a counter-intellegence agent, which MOS is better to start, 31B or 35F?

Go 35F, it'll expose you to the Intelligence Community (IC). See what's out there and don't be in such a hurry to settle down just yet.. And spell intelligence correctly...

35F for a number of reasons. You have the same clearance level as a 35L, this is one of the biggest hurdles those re-classing today. 35F also gives you the analytical side of military intelligence.

35F really helps with analytical skills, as well as learning the most effective way to research.