It's subjective of course, but Mara does seem to have been more popular overall. I mean Lucasfilm never bothered to hire an official Thrawn "model" and one assumes they only did so for her (and no other character) to meet the demand for Mara Jade merchandise. She was also around in a lot more stories. Thrawn's still pretty up there in terms of popularity (even before his canonisation.) Indeed if one were to do a poll of people's favourite EU characters, I think it's a safe bet both Thrawn & Mara would be somewhere in the top 5, if not top two or three alongside Jaina Solo.