The thresher maw that ate the reaper on Tuchanka was considered the "mother of all thresher maws" by the Krogans. Whether or not it actually is the source of all other thresher maws in the galaxy is debatable, but one thing that this 'maw is is HUGE. While the thresher maw you fight in Mass Effect 2 is big (or probably the same size as the ones seen in Mass Effect), this "mother" was larger than the Destroyer Reaper it took down, which in turn was much larger than the 'maw you fought in ME2.
Also note that the Mother 'Maw physically grappled with the Reaper, pulling it to the ground and then under the sands. When fighting Reapers with ships the weapons used are all solid projectiles or molten metals propelled at near light speeds with very high associated energies. While a Reaper's kinetic barriers are able to easily defend against these high energy attacks they probably aren't optimized to withstand a (relatively) low energy wrestling match.