Considering the nature of the War on Drugs I'd expect most of the expenditure to be at the local and state level, but the biggest chunks at the federal level aside from the DEA's budget would probably be the proportion of Coast Guard and CBP time and resources dedicated to counter-drug operations and the military and policing aid given to countries like Mexico and Colombia. This is a bit hard to quantify though, as the Coast Guard and CBP usually conduct counter-drug operations as part of their usual duties and not all the aid being sent to Colombia and Mexico is motivated solely by the desire to contain drug production and shipment.
So you would not necessarily find the remaining funding hidden within the federal budget.