We use Minkowski Functionals (MF) to constrain a primordial non-Gaussian contribution to the CMB intensity field as observed in the 150 GHz and 145 GHz BOOMERanG maps from the 1998 and 2003 flights, respectively, performing for the first time a joint analysis of the two datasets. A perturbative expansion of the MF formulae in the limit of a weakly non-Gaussian field yields analytical formulae, derived by Hikage et al. (2006), which can be used to constrain the coupling parameter f_NL without the need for non-Gaussian simulations. We find -1020<f_NL<390 at 95% CL, significantly improving the previous constraints by De Troia et al. (2007) on the BOOMERanG 2003 dataset. These are the best f_NL limits to date for suborbital probes.