'Boondock Saint' -- The $64,000 Tax Question

Sean Patrick Flanery -- who played one of the trigger-happy MacManus brothers in "Boondock Saints" -- may have more of the Lord's work to be done ... because the actor allegedly owes more than $64k in back taxes.

According to paperwork issued by the State of California Franchise Tax Board -- Flanery stiffed the broke-ass Golden State out of $64,684.38 between 2003 and 2008.

We called Flanery's peeps for comment -- so far, we got nothin'.