I'm a US native speaker, and in the US both pronunciations are common and normal.
My personal favorite dictionary for US English, is the American Heritage Dictionary. I just checked, and it shows three pronunciations, and they are always listed in order of frequency: (ĭn´trĭst, -tər-ĭst, -trĕst′). So according to this dictionary, two syllables is more common than three... and there is variation in the vowel sound in -est.
It might depend on context and euphony.
I'm not sure, but if were saying "Please tell me some of your personal interests" I think I would pronounce "interests" as three syllables. If I were saying "The Fed raised the interest rate today" I would probably use two.